The decision, handed down in Quebec Superior Court, came at the 11th-hour for Leon Mugesera, who was slated for deportation to Rwanda on Thursday from Canada.
Justice William Fraiberg ordered a stay of deportation until Jan. 20, when Mugesera's lawyers are due back in court.
The lawyers who filed the motion on Mugesera's behalf said they had never even met the man, but were upset at what they deemed to be flippant behaviour by the federal government.
They say the Canadian government's international obligations require it to keep Mugesera here while the United Nations Committee Against Torture examines his case.
Ottawa expressed surprise and disappointment with the ruling, saying it was weighing its legal options. The government is not obliged to comply with the provincial court order, one of Mugesera's lawyers said.
Mugesera is expected to face criminal charges in Rwanda related to the 1994 killing of between 800,000 and one million Rwandans.
Earlier this week, the Federal Court rejected Mugesera's last-ditch effort to stay in Canada, his home for the last 19 years, and he was set to be deported immediately.
But that decision was followed by a flurry of surprising developments — including the provincial court order and Mugesera's sudden hospitalization for an unspecified health issue.
Mugesera's family said Thursday that he was in "critical condition" in a Quebec City hospital, where he spent a second straight day. Media reports said he might have ingested medication that made him ill, following his deportation order Wednesday.
Television images showed a bundled Mugesera laid out on a stretcher as he was wheeled out of his Quebec City home.
"Dad is in critical condition," Mugesera's family said in a statement released by his lawyer's office. The family did not provide any further details about his condition.
A university professor and one-time Rwandan political operative, Mugesera gave a virulent, anti-Tutsi speech in 1992. Two years later, Hutu-backed militias later carried out a 100-day massacre of Tutsis and Hutu moderates.
If the deportation order is carried out, he would become the first Western refugee claimant to be sent back to Rwanda to face charges related to the genocide.
Mugesera, however, says he could be tortured if he's sent back to Rwanda.
To complicate matters, the United Nations Committee Against Torture requested that Canada keep Mugesera here while it investigates his claims he'd be tortured in Rwanda.
His family also pleaded with Ottawa to give the international body the time it needs to complete an investigation, which could take at least a couple of months.
"We implore Canada to respect its international obligations as demanded by the (UN) High Commissioner for Human Rights on Jan. 11, 2012," the family said in the short statement.
That UN-related request is what prompted the last-minute challenge Thursday in provincial court.
"Our argument is that if it has any meaning for Canada to ratify these international conventions, then they should wait instead of acting like cowboys," said lawyer Philippe Larochelle, who is scheduled to debate the case in Superior Court next week.
"They were not obliged to ratify the international convention against torture, but if they do so then it should have some meaning in Canadian law."
Larochelle said his team's Superior Court challenge had little to do with the specifics of Mugesera's case — it was about holding Canada accountable for its commitments.
"My problem is not Rwanda or Mugesera, it's these people in power right now," he said, referring to the Conservative government.
"It's a Kyoto (Protocol) kind of a thing. We spent considerable amounts of money creating a legal context, which sort of reflects what the UN and what other international institutions think, and then after that we just flush it all down — which I think is a bit shocking."
A spokesman for Public Safety Minister Vic Toews said the federal government still intends to remove Mugesera from Canada as soon as possible — depsite Thursday's court order.
"We are extremely disappointed with this surprising ruling," Michael Patton wrote in an email.
"We are examining our legal options."
Mugesera has been locked in a lengthy legal battle against Ottawa for the right to stay in the country — a fight that wound up before the Supreme Court of Canada in 2005.
His lawyer, Johanne Doyon, has said she's now waiting for the federal government to react to the UN's non-binding request.
Doyon says if the UN finds that Mugesera is at risk of torture in Rwanda, he could stand before a genocide-related trial in Canada.
But Ottawa signalled Wednesday that it intends to carry out the deportation order.
"War criminals will find no haven on our shores," the government said in a statement, adding that Mugesera would be removed as soon as possible, "in accordance with Canadian law."
The federal government has disputed the warnings of possible torture, saying it has taken all necessary steps to ensure Mugesera would be treated fairly in Rwanda.
Federal Court Judge Michel Shore's 28-page decision, handed down Wednesday, agreed with the government assessment.
Recent decisions by the European Human Rights Court and the International Criminal Tribunal for Rwanda, which have ordered the transfer of alleged war criminals to that country, further confirm Rwanda's credibility, Shore noted.
The director of the Montreal Institute for Genocide and Human Rights Studies said the Canadian government should give the UN time to investigate — particularly since the world is watching Mugesera's landmark case.
"It would set a great example and I don't think a delay of two months is going to make that much of a difference," said Frank Chalk, also a Concordia University history professor.
"Equally, this will put more pressure on Rwanda to show that it respects human rights."
Chalk said Rwanda has taken huge strides toward improving its human-rights record over the last five years.
With the help of Canadians, he said the country has trained new judges who have been encouraged to remain independent of the government. He also said the death penalty has been removed and prison conditions are vastly improved.