The awards – France’s equivalent of the Oscars – have been mired in controversy after Polanksi’s An Officer and a Spy received 12 nominations.
The Polish-French director fled the US after his rape conviction in the 1970s.
He has since faced other accusations of sexual assault.
An Officer and a Spy, or J’accuse in French, is about the Dreyfus affair in 19th Century France and won a total of three awards on Friday night.
Polanski and members of his crew did not attend the event, with the director having said previously that he feared for his safety.
The prize for best film was awarded to Les Misérables by director Ladj Ly.
Actress Adèle Haenel, who has said she was sexually abused as a child by another director, was one of the women who walked out of the ceremony after Polanski’s win was announced.
She left the room saying “shame!”, and was followed by director Céline Sciamma.
Actress and comedian Florence Foresti, who was presenting at the ceremony, did not return to the stage after Polanski’s award was announced. She later updated her Instagram story to a black screen with the word “disgusted”.
Hours before the ceremony began, France’s Culture Minister Franck Riester said it would be “symbolically bad” if Polanski were to win the prize for best director, “given the stance we must take against sexual and sexist violence”.
Protesters also gathered outside of the venue ahead of the awards.
The decision to honour Polanski at this year’s awards had angered feminist groups and led to calls for a boycott.
The César’s entire board resigned earlier this month amid the backlash. A general meeting is set to be held after the ceremony to elect a new board, which will look at implementing reforms and modernising the institution.
France’s equality minister, Marlène Schiappa, had previously condemned the decision to nominate Polanski’s film, saying she found it “impossible that a hall gets up and applauds the film of a man accused of rape several times”.
But the Césars defended the nominations, arguing that the body “should not take moral positions” in giving awards.
Polanski himself told Paris Match in December that he had tried to distance himself from the calls for a boycott of his film. “For years people have tried to make me out as a monster. I’m used to the slander and I’ve grown a thick skin, which is as hard as a shell,” he said.