Polanski is still wanted in the United States for the statutory rape of a 13-year-old girl in 1977.
In a clip of Haenel right after her exit, she sarcastically chants "Bravo la pédophilie" ("Bravo pedophilia") while continuing to walk away from the event.
At the announcement of Polanski's award as best director, boos emerged from the public composed of film teams and cinema professionals.
Portrait of a Lady on Fire is now in select theaters.
Outside the venue, hundreds of people had gathered to protest Polanski and the industry that continues to celebrate and protect him.
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And as a part of his visit, he addressed the massive crowd at world's largest cricket stadium - Motera Stadium. Former English professional footballer Gary Lineker was also not happy with Trump's pronunciation.
An Officer and A Spy also won Cesars for Adapted Screenplay and Costume.
The film was nominated for 12 awards.
As the ceremony unfolded, protesters outside clashed with police as they tried to enter the building.
Host of the ceremony, Florence Foresti, later posted an Instagram story with a black screen and the word: "Disgusted". Polanski has been a fugitive since 1978, when he fled the country while awaiting sentencing for his sexual abuse case.
Last year, a woman came forward to accuse Polanski of raping her in 1975 in his Swiss chalet when she was 18.
"The parallel that is made between the anti-Semites who attacked Dreyfus and feminists of today who fight for equality between men and woman and the end of impunity for sexual offenses is simply disgusting", Celine Piques, of activist group Osez le Feminisme, told The AP. Polanski has denied the accusation. He has since been accused of rape and sexual assault by several women, many when they were minors.
The Cesar for best film was awarded to Les Miserables, Ladj Ly's Oscar candidate, about tensions between police and minorities in a poor Paris suburb.