"It's very nice that you've been shooting so many movies in Europe, even if you are not being convicted for rape in the US," said master of ceremonies Laurent Lafitte.
"Thank you for coming tonight, sir. But it's good, because you give badly-paid bit parts to French actors, which kind of puts them in their place," he added.
The director, 80, whose film opened the festival, was sitting in the front row at the time Lafitte made the joke, which drew gasps from the audience, reported Variety.
Allen is accused of sexually abusing his adopted daughter Dylan with ex Mia Farrow but there were no charges against him.
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The allegations resurfaced when Dylan recalled the incident in a letter to the New York Times in 2014.
Allen also wrote an open letter, where he called the accusations ludicrous. He maintains that Farrow coached the child, then 7, during their bitter split.
He was involved with Farrow's adopted daughter Soon-Yi Previn, who was 21 at the time of the scandal. They later married in 1997.