Dolan's film, Laurence Anyways, was nominated in the Best Foreign Film category but Affleck took the title with his critically acclaimed film Argo.
This was the third time Dolan has had his work nominated for a Cesar Award.
Austria's celebrated film, Amour, directed by Michael Haneke, took five trophies, including Best Film, Best Actress and Best Actor.
Amour is up against Quebec filmmaker Kim Nguyen's Rebelle/War Witch for Best Foreign Film at the Oscars on Sunday.
Here is a list of the night's winners: