"Joker" is loosely based on the popular DC supervillain of the same name. It follows the life of Arthur Fleck (essayed by Phoenix) as an aspiring stand-up comedian and his transition into becoming the Joker.
In his acceptance speech, director Todd Phillips thanked Warner Bros. and DC for stepping "out of their comfort zone and taking such a bold swing on me and this movie", reports dailymail.co.uk
"There is no movie without Joaquin Phoenix. Joaquin is the fiercest and brightest and most open-minded lion I know. Thank you for trusting me with your insane talent," he added.
The 76th edition of the film fest wrapped up on Saturday night.
Phoenix's "Joker" had its world premiere in Venice on August 31. The movie will release in the US on October 4.
A sequel is said to be in the works, as well as a film which would see Phoenix's Joker encounter Robert Pattinson, who has replaced Ben Affleck as Batman.
The second prize, the Silver Lion award, went to Roy Andersson, who won it for Best Directing for "About Endlessness".
Though inclusion of Roman Polanski's "An Officer and a Spy" raised many questions, the film was received warmly in Italy. It was announced as the early winner of the FIPRESCI prize.