Munyaneza was the first person to be tried under Canada's Crimes Against Humanity and War Crimes Act, which allows residents to be tried for crimes committed abroad.
Munyaneza's two-year trial heard from 66 witnesses in Canada, France, Rwanda and Tanzania.
The court was told that Munyaneza, the son of a wealthy Hutu beer distributor, set up roadblocks in southern Rwanda to select Tutsis and moderate Hutu as victims based on their ethnicity or allegiances.
One man who was imprisoned in Rwanda for his own role in the genocide testified that Munyaneza orchestrated the massacre of between 300 and 400 Tutsis in a church.
"The accused's criminal intent was demonstrated beyond a reasonable doubt, as was his culpable violence," Denis wrote in his judgement.
The UN estimates that more than 800,000 people were killed during the violence.
"I'm very happy he was found guilty. I want to thank and congratulate Canada," Caesar Gashabeze, a survivor of the genocide, said.
"We have been waiting for this."
The defence said it would appeal the conviction after repeatedly questioning the testimony of witnesses and highlighting the fact that most were unable to identify Munyaneza's prominnent facial scar.
"The evidence did not justify a conviction," Richard Perras, Munyaneza's lawyer, said.
Munyaneza was arrested in Toronto in 2005 after seeking asylum in Canada, which Canadian immigration officials rejected. He had fled to Cameroon after the genocide.
The prosecutor said that the case illustrated Canada's commitment to bringing war criminals to justice.
"The case was very challenging as it involved events dating back 15 years in a foreign country, Rwanda," Pascale Ledoux said.
Munyaneza will be sentenced in September.