The ruling by Judge Richard Mosley means Khadr can significantly expand his $20-million civil lawsuit in which he accuses Ottawa of complicity in what he claims was his arbitrary detention and cruel and inhuman treatment at the hands of the Americans.
"Whether Canada conspired with foreign officials to violate the fundamental rights of a citizen is not a trivial matter," Mosley said in his ruling.
"If anything, adding conspiracy to the statement of claim clarifies the nature of the controversy between the parties and facilitates its comprehensive examination by a court."
The federal government had opposed the expanded claim, arguing among other things that international law bars Khadr from dragging the U.S. into his civil action, first filed in 2004.
Mosley said it should be up to a trial judge to decide whether the conspiracy allegation can stand.
He said Khadr's action does not name the U.S. as a defendant nor seek any remedy that could be enforced against American authorities. As a result, it does not violate rules against domestic courts pronouncing on actions by foreign governments, Mosley said.
He awarded costs to Khadr's lawyers on the grounds that Ottawa had "considerably increased the costs and delay" of the action by opposing the lawsuit amendments, almost all of which he allowed.
Among other things, documents show Canadian agents went down to the infamous U.S. prison in 2003 and 2004 to interrogate the Toronto-born Khadr after first agreeing to share any intelligence with his American prosecutors.
Khadr's military captors then subjected him to sleep-deprivation — known as the "frequent flyer" program — to soften him up for interrogation by the Canadians, previously released documents show.
Mosley himself noted three U.S. Supreme Court decisions found procedures at Guantanamo Bay while Khadr was detained to be illegal.
Khadr's lawyer John Phillips said he was pleased the conspiracy claim could now go ahead as part of the lawsuit.
"This will allow for a full hearing and full airing of what happened to Omar and how he was treated by both the United States and Canadian government authorities," Phillips said.
"We're going to see justice done."
None of Khadr's claims has been proven in court.
The U.S. government has denied torturing Khadr, 28, who pleaded guilty to five war crimes in October 2010 before a widely maligned American military commission for incidents that occurred in Afghanistan when he was 15.
In return, he was handed a further eight-year sentence. He later said he pleaded guilty only to get out of Guantanamo Bay and come back to Canada.
The Americans had arrested him in July 2002 following a brutal firefight in which he was terribly injured and an American special forces soldier was killed. He was finally returned to Canada in September 2012 and is currently incarcerated in Alberta.
While Ottawa maintains Khadr is a hardened terrorist, legal experts have argued his actions could not have amounted to war crimes under international law.