Toronto-born Khadr returned to Canada on Saturday after 10 years in the notorious U.S. prison at Guantanamo Bay, a facility which has been condemned by human rights organizations across the globe.
The Harper government has been accused of dragging its feet on the 26-year-old's case and Canada's foreign affairs minister even recently suggested the repatriation came after diplomatic pressure from the U.S.
But Jacobson, who spoke to reporters at Ottawa's Carleton University after a speech on the upcoming American presidential election, said Canada and the U.S. collaborated on the Khadr file.
"I'm not sure I'd use the word pressure. We wanted it to happen. We had an understanding with Canada that's public — the fact that they would look favourably on a request," he said.
Jacobson called Khadr's return a small step towards the eventual closure of the prison because the Canadian citizen was the last Western national held there.
U.S. President Barack Obama promised to close Guantanamo Bay four years ago when he won the White House, but Jacobson said Obama has faced serious obstacles.
"Is it the end of the road? No. This has been a difficult thing for the president. He indicated on day one ... that he was going to try to close Guantanamo. He has met a lot of resistance in Congress and elsewhere. But this was a step in the right direction and we're pleased the Canadians did it," said Jacobson.
"We explained to the Canadians our desire. But we don't pressure, that's not how it works."
On Sunday, Foreign Affairs Minister John Baird simply answered "yes" when asked by CTV's Question Period if the U.S. had exerted diplomatic pressure on Canada to accept Khadr.
Baird added that since Khadr is a Canadian citizen and the Americans plan to close Guantanamo Bay, Canada did not have much of a choice but to let the prisoner return.
Khadr pleaded guilty in October 2010 to five charges, including murder in violation of the law of war for the death of an American special forces soldier in Afghanistan in July 2002. Khadr was 15 years old at the time of the offences.
Under the terms of a plea agreement, Khadr was eligible to return to Canada a year ago to serve out the remainder of an eight-year sentence for war crimes, but his transfer was delayed amid sniping between Canada and the U.S.
Public Safety Minister Vic Toews had insisted he needed to satisfy himself that Khadr would pose no threat to public safety.
Speaking in the House of Commons on Monday, Toews said Khadr's weekend repatriation came after a regulatory process was followed.
"The transfer of Omar Khadr occurred following a process initiated by the American government and conducted in accordance with Canadian law. It did not include consideration of foreign relations," he said.
Meanwhile, interim Liberal leader Bob Rae said the rhetoric used by the Conservatives to portray Khadr to Canadians needed to change.
"I think the attitude of the Conservatives is completely out of keeping with what needs to happen and where we need to be as a country with respect to Mr. Khadr," Rae said.
"But we’ve come to expect nothing else, nothing less, nothing better from the Conservatives or from Mr. Toews...they’re going to continue to use what I call simple cartoon rhetoric and cartoon language in describing a real person who now has to be rehabilitated into Canada."
The U.S. had little to say about Khadr's transfer prior to Jacobson's comments Monday night.
"We're glad that it's behind us. We appreciate the actions of Canada," Jacobson said.
Khadr was taken to Millhaven Institution west of Kingston, Ont., upon his return for a period of assessment — a normal procedure for new inmates — before authorities decide where he will serve out the remaining six years of his sentence.
He will be eligible for parole within about six months.
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