Dylan Farrow, Allen's adopted daughter with former wife Mia Farrow, accused the director of sexually abusing her in the early 1990s while she was a child.
She reiterated her claims in a 2014 New York Times op-ed and other articles.
The allegations caught steam in the wake of the #MeToo uprising.
The "Call Me By Your Name" director disapproves of Allen's dismissal from Hollywood courtesy of #MeToo allegations brought forth again, over 20 years after he was found not guilty in the court of law.
Speaking with IndieWire, Guadagnino called it "the perverted and primordial enjoyment of a kind of 'Scarlet Letter' trial of a man.
"I still am a believer in state of rights; Mr Allen went through many investigations 20 years ago and was cleared. The Woody Allen legacy - those movies are there, and they are fantastic. Anyone who denies that 'Another Woman' is masterpiece is stupid!' he added.
The director made his Cannes Film Festival debut this year with the short film, "The Staggering Girl".
He asked Ariel Schulman to draw the title font of the film by hand as it happens in Allen's films.
"I'm a Venice (festival) man. I am a nouvelle vague person, this is my first time. I felt at home. Maybe this is the beginning of a new phase for me," he added.
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