Jones told CBC News he may appeal. But for the time being, he said he would head back to Florida.
The Canada Border Services Agency made Jones go through a secondary inspection when he arrived at the Ambassador Bridge in Windsor, Ont., around noon. Secondary inspection involves a search of a person's vehicle and more extensive questioning.
He was held there for several hours before being told he would not be allowed into Canada. Jones said the CBSA cited a previous peace bond infraction in the U.S. as well as an incident relating to a disputed honorary doctorate in Germany to keep him out. "The reasons are pretty bogus in our opinion," he said.
Jones said the border officials, who he described as "cordial", asked him about "the hate speech aspect" of his Toronto appearance.
"Definitely, the concern was ... that rally we were to attend and speak at," he said.
Jones called the decision to bar him a "grievous act" and said it was unwarranted in a country "that is supposed to have freedom of speech."
"I think to ban you from a country…I think there has to be more serious charges," he said. "I think you have to be a criminal or pose some type of threat to national security."
No confirmation from CBSA
The CBSA refused to confirm that Jones was banned. "It is not our practice to confirm/deny whether any one person has sought entry/entered Canada," said a statement emailed to CBC News.
"Several factors are used in determining admissibility into Canada, including involvement in human rights violations, in organized crime, in criminal activity, security, health or financial reasons," the agency said.
"Planning to attend an event in Canada is not itself grounds for being inadmissible."
The pastor was on his way to a scheduled speaking engagement on the lawn of the Ontario legislature at 6 p.m. Thursday. Organizers said the event will go ahead despite Jones' absence.
The event is titled "Canadians united against terror." It was to include a memorial for U.S. Sgt. 1st Class Christopher Speer. Canadian Omar Khadr pleaded guilty and was convicted of the murder of Speer, a soldier who died from his wounds during a firefight in Afghanistan in 2002.
A discussion was to follow dealing with the anti-Islamic video Innocence of Muslims. The film sparked protests and outrage throughout the Middle East. Organizers said the video would not be shown at the event. Instead, a panel discussion would broach the issue of whether it should be shown.
Jones is best known for burning a Qur'an on the anniversary of the 9/11 terrorist attacks.
Proposed bill tightens border
Citizenship and Immigration Minister Jason Kenney's office told CBC News the government did not have the power to keep Jones out of the country.
That decision lies solely with the CBSA, which can keep Jones out of Canada if he's considered a security threat.
The Conservatives have proposed a bill that would make it much easier to keep such people out of Canada.
Bill C-43, the Faster Removal of Foreign Criminals Act, would give the immigration minister powers to determine who can be kept out of — or allowed in — the country.
One measure of the bill would give the minister the power to deny someone entry or temporary resident status for up to three years on the basis of public policy considerations.
The NDP's border critic, Brian Masse (Windsor West) has issues with the bill, including its name.
"It is unfortunate that these types of titles have now been introduced into legislation. This one is very serious. It is a continuation of our immigration drift," Masse said in the House last week.
Kenney said last June that the power would be used sparingly.
"This is an important initiative to protect Canadians from serious, repeat foreign criminals who have been delaying their deportation from Canada and in too many cases going on to create new offences and create new victims in Canada," Kenney said outside the House of Commons when the bill was introduced in late September.
The bill would also ease the way to deport refugees, permanent residents and visitors for "serious criminality," crimes where the punishment is six months or more in jail.