"I feel a lot of emotions, I wasn't sure if people would have understood what we were trying to do with @jokermovie. Now I'm sure everyone here has understood. We are very proud of this film," Phillips said as he accepted the award with Phoenix by his side.
The movie is set for release in the United States on Oct. 4.
Roman Polanski's J'accuse won the Silver Lion Grand Jury Prize, Roy Anderson won the Silver Lion Award for Best Director for About Endlessness, Ariane Ascaride was named Best Actress for Gloria Mundi and the Best Actor honor went to Luca Marinelli for Martin Eden.
Variety said Polanski's wife, Emmanuelle Seigner, accepted his award on his behalf.
Polanski has been a fugitive from the U.S. justice system since 1978 when he pleaded guilty to the statutory rape of a 13-year-old girl, then fled the country before he could be sentenced.