Zakaria Amara, 24, received a life sentence "for his role in a terrorist plot to bomb Toronto," the Public Prosecution Service of Canada said in a statement.
He also he was sentenced to nine years "for his participation in a terrorist group," to be served concurrently.
The sentence is the stiffest punishment imposed in the conspiracy and under Canada's anti-terrorism laws, which parliament passed in the wake of 2001 attacks on the United States.
Amara may however be eligible for parole in less than seven years after having already served time in prison awaiting trial.
"What this case revealed was spine-chilling," said Justice Bruce Durno in court, his remarks cited by The Globe and Mail newspapers.
"It cannot be said these things happen only in other countries," he said. "These things happen here."
Zakaria last week apologised to Canadians for his actions in an open letter he read in court.
"I deserve nothing less than your complete contempt," he said in his first public remarks.
The mastermind of an Al-Qaeda inspired plot to bomb the Toronto Stock Exchange, Canada's spy agency offices and a military base using fertiliser explosives packed in rented trucks said his interpretation of Islam was "naive and gullible."
But his outlook changed in the years he spent in prison awaiting trial, he said.
Amara, a Sunni Muslim, explained he befriended a Jewish inmate and a Shia Muslim who helped turn him around, as well as a banker who once worked in the Toronto Stock Exchange building.
"When someone shows me I'm wrong," he said, "I'm willing to accept it."
But Ontario Superior Court Justice Durno ruled Amara "did not just commit a criminal offence. He committed a terrorist offence that would have had catastrophic consequences. He did not serve as a foot soldier but as a leader."
Earlier, a co-conspirator Saad Gaya, 21, was sentenced to 12 years in prison for his role in the foiled 2006 bomb plot aimed at provoking a Canadian withdrawal from Afghanistan.
Gaya pleaded guilty to the "terrorism" charges in September.
Another of the plotters is currently on trial while charges against seven others were dropped and five still face trial.
They were arrested during a police sting operation in 2006 and charged with participating in a "terrorist" group and attempting to "cause an explosion."
Specifically, they aimed to "acquire explosive substances and cause an explosion or explosions for religiously-inspired political purposes," said court documents in the Gaya case.
Members of the group allegedly sought to purchase three tonnes of the bomb-making ingredient ammonium nitrate from undercover police officers, who had switched it with an inert substance.
Gaya's motivation "was to pressure Canada into withdrawing troops from Afghanistan, the religious aspect being to protect a Muslim country from attack," said prosecutors.
His lawyer Paul Slansky told reporters after his sentencing: "Terrorism is a terrible and heinous crime but not everyone that commits a heinous and evil crime is themselves evil.
"I do believe that he was a misguided youth who made some seriously erroneous mistakes in deciding to trust these people who were themselves misguided," he said.
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