Berlin police said they were called into the small business near the city centre after someone inside recognized Magnotta, who was at a terminal surfing on the Internet.
A department spokesman said Magnotta initially tried to give officers false names, but then conceded: "OK, you got me."
CAUTION: GRAPHIC CONTENT MAY DISTURB SOME READERS.
Magnotta, 29, is facing five charges in Montreal, including first-degree murder, in the brutal slaying and dismemberment of Jun Lin, a Chinese national who was studying at Concordia University.
His capture came less than a week after police issued a warrant for his arrest in connection with Lin's death — a macabre killing that grabbed international headlines and shocked people around world.
Lin's torso was found stuffed inside a suitcase on a Montreal curb outside Magnotta's apartment building last Tuesday. Other body parts, including a hand and foot, were mailed separately to the offices of political parties in Ottawa.
Montreal police said Magnotta fled Canada for France about a day after Lin's death, which is believed to have occurred sometime overnight between May 24 and May 25.
Magnotta was seen in Paris over the weekend — more than 1,000 kilometres from Berlin — and, after several days of police work from forces on two continents, authorities finally apprehended him without incident.
"He did not resist," Chief-Supt. Stefan Redlich of Berlin police told The Canadian Press in a phone interview.
"He was arrested without a fight."
The owner of the cafe, in Berlin's working-class Neukoelln district, told The Associated Press that Magnotta had come in to read online news reports about himself when one of his employees thought he looked familiar.
"A colleague recognized him from his photo, because he'd just read the newspaper," said the owner, who spoke on condition he not be identified by name.
He said police happened to be outside at the time, and the employee alerted them.
Time-stamped footage from the cafe's security camera suggests Magnotta was inside at a computer for around two hours before seven police officers were seen moving quickly through the front door.
A couple of minutes later, the footage showed three officers escorting a handcuffed, calm-looking Magnotta, who was sporting sunglasses.
Magnotta, who grew up in Scarborough, Ont., was taken to a German prison and is expected to see a judge on Tuesday. German authorities are expected to contact Canadian officials to determine how to proceed with his extradition.
There is also some irony in the fact Magnotta was arrested while reading news stories about himself at an Internet cafe. For years, he posted personal images online and authored web writings to feed his own prolific Internet presence.
''He used the web to glorify himself but it was also the web that helped in his arrest,'' Montreal police Cmdr. Ian Lafreniere told reporters Monday, referring to photos of Magnotta that were circulated worldwide.
It's unclear, however, when Magnotta will actually set foot on Canadian soil.
"It could take a very long time," said Rene Verret, a spokesman for Quebec's bureau of prosecutions.
Verret said his office will send a request in the coming days to Canada's federal justice minister for Magnotta's extradition, asking that it be forwarded to German officials.
He said if Magnotta doesn't contest the order, the suspect could be returned to Canada within a couple of weeks.
But if Magnotta fights the extradition the process could take years, Verret said, referring to the case of German-Canadian and former arms-industry lobbyist Karlheinz Schreiber.
Schreiber was arrested in Canada in 1999 under a German warrant and was only sent to Germany in 2010 after a lengthy battle against extradition.
A spokeswoman for Justice Minister Rob Nicholson said officials are "working expeditiously" to prepare necessary materials for the extradition request.
The grisly case has captured significant international attention and media abroad have dubbed Magnotta, a porn-flick actor, the "Canadian Psycho," the "Canadian Cannibal" and the "Carver from Montreal."
Interpol had issued an international alert and circulated photos of Magnotta, who was born Eric Clinton Newman and has also used the name Vladimir Romanov.
A Toronto lawyer who represented Magnotta in a fraud case in 2004 and a sexual assault case in 2005 remembered him as soft spoken and polite.
"I've had lots of creepy characters and Eric did not stand out as one of them," said Peter Scully.
Magnotta was charged with a dozen counts of fraud and impersonation for using a woman's credit card to buy about $17,000 worth of goods, Scully said. He pleaded guilty to four fraud-related charges and received a nine-month conditional sentence and a year of probation.
Scully said Magnotta was charged with sexually assaulting a woman in 2005, but the prosecution decided to withdraw the charges.
Magnotta is now facing other charges in Canada, including corrupting morals; causing an indignity to a body; using the mail system to deliver "obscene, indecent, immoral or scurrilous" material; and harassing Prime Minister Stephen Harper and some MPs.
Some of the charges come in connection with an incident that saw a package containing a severed foot delivered to the Conservative party's Ottawa headquarters. A parcel containing a hand was also addressed to the Liberal party, but it was intercepted by Canada Post workers before delivery.
Harper commended police on Monday for catching Magnotta.
"Well, I'm obviously pleased that the suspect has been arrested, and I just want to congratulate the police forces on their good work," the prime minister said in London, where he was attending the Queen's Diamond Jubilee.
Back in Montreal, Lin's former boss said there's no way to bring the 33-year-old back, but he's glad the suspect has been arrested.
"I feel like there is justice — it does exist," said Kankan Huang, owner of a convenience store where the computer-science student had worked part-time as a cashier since last August.
"This guy is going to pay (for) what he did."
A memorial to Lin was posted inside Huang's store Monday. It featured flowers and around a dozen sympathy cards written in English, French and Mandarin.
Huang said members of Lin's family, who live in China, are expected to visit him at his shop in the coming days.
The public's horror over Lin's death increased after police said the killing was videotaped and posted online.
In the video, a person repeatedly stabbed a young man with an ice pick. The killer dismembered the corpse and appeared to commit sexual and cannibalistic acts on it.
Police allege the depraved events took place in Magnotta's cramped bachelor apartment, which he rented for $490 per month in a gritty building in west-end Montreal.
The day after Lin's torso was found locked in a suitcase, the building's tenants were trying to cope with the disturbing crime in their midst. Others had to clean up the ghastly mess in blood-soaked Apartment 208.
Police had left behind a pink bed sheet, a purple shower curtain and a mattress, all of which appeared to be stained with blood.
A liquid, which looked like dried blood, had pooled at the bottom of the unit's small refrigerator. A few tiny bits of what appeared to be flesh were still stuck to the inside walls of the appliance.
Magnotta, who has worked as a model and a low-budget porn actor, has maintained a prominent profile in the darkest corners of the Internet.
For nearly two years, he has been a notorious figure among animal-rights activists who have been looking for a man who tortured and killed cats and then posted videos of the acts online.
He has also been romantically linked to sex-killer Karla Homolka — a rumour he has vehemently repudiated and others have shrugged off.
A Facebook page belonging to a self-described model with the same name lists a variety of personal heroes. They include pop star Madonna and two Russian leaders: Vladimir Putin and Joseph Stalin.
Magnotta has also been an avid author on the Internet.
One online article he wrote in 2009 was titled: "How to Completely Disappear and Never Be Found." It shares a six-step process for escaping and shedding one's identity.
But his time on the lam came to an end Monday after he left a heavy scent on his European getaway trail.
Over the weekend, numerous reports linked Magnotta to Paris, with sightings and evidence found at various places.
French media reported Sunday that personal belongings believed to be Magnotta's were found in a hotel in a city suburb. Those reports said police discovered pornographic magazines as well as air sickness bags from the airplane he took to Paris from Montreal.
He remained in France until at least Friday, Montreal police confirmed. There were reports that Magnotta had boarded a bus for Berlin late last week.
Shockwaves from Lin's death were also felt far beyond Europe.
Lin's slaying prompted the Chinese Embassy in Ottawa to issue a statement advising Chinese visitors to Canada to take safety precautions.
A spokesman for China's foreign ministry reiterated the warning Monday and extended the government's condolences to Lin's family.
"The methods used in the crime were brutal,'' Liu Weimin told a news conference in Beijing. ''The nature and impact of this crime were utterly horrible and we feel deeply shocked."
He said Chinese diplomats have stayed in close contact with police and officials in Canada.
Chinese students and other Chinese nationals in Canada should "increase their awareness of self-protection and strengthen safety precautions," he said.
Liberal interim leader Bob Rae said while Canada is a relatively safe country, the Lin case is a reminder that it is not immune to the "terrible forces that are at work in our societies."
Rae added that with all the publicity around the crime, one must not forget that a man has died in "absolutely appalling circumstances."
— With files from The Associated Press in Berlin, and Canadian Press reporters Sidhartha Banerjee and Pierre St-Arnaud in Montreal and Steve Rennie in London.