It was the fifth time Polanski had won the prize and it sparked an angry backlash.
One of France's most prominent actresses stormed out of a film awards ceremony after Roman Polanski won the best director gong.
Adèle Haenel left the room at the 45th César Awards — France's Oscars — after the filmmaker was recognised for An Officer and a Spy (J'accuse).
Polanski, 86, is still wanted in the United States decades after he was charged with raping a 13-year-old girl in 1977. He pleaded guilty to unlawful sexual intercourse with a minor but fled the country on the eve of sentencing.
Haenel, the symbol of a new impetus of #MeToo in France since she accused director Christophe Ruggia in November of "repeated touching" when she was a teenager, shouted "shame" as she left the room on Friday evening.
She was followed by director Céline Sciamma and a few others, just before the César announcement for best film.
It was the fifth time that Franco-Polish filmmaker Polanski had won this prize, having received it for Tess in 1980, The Pianist in 2003, The Ghost Writer in 2011 and Venus in Fur in 2014.
An Officer and a Spy is a historic thriller about the Dreyfus Affair. In September, Polanski's movie won the Grand Jury Prize at the Venice Film Festival.
Florence Foresti, who was presenting the ceremony, posted on Instagram that she was disgusted after Polanski won.
Refusing to name him, she had called the filmmaker "Sneezy" several times during the evening in allusion to the Snow White dwarf.
French feminist organisation Osez le féminsime! tweeted: "Best director for Polanski: the room is shocked. Silence and embarrassment. The Césars of shame!"
Before the ceremony, hundreds of demonstrators, mostly women, protested outside the ceremony in Paris.
Two protesters were arrested, a police source confirmed to AFP.
Less than two hours before the start of the ceremony, demonstrators with smoke bombs tried to approach the concert hall shouting "lock-up Polanski".
Protesters who tried to break down barriers were pushed back by the police.
The demonstrators launched slogans against the filmmaker like "Polanski rapist, guilty cinema, and public accomplice". There were other posters that read: "Victims of Polanski, we believe you" or "Down with the patriarchy".
Roman Polanski and the film's team, including actor Jean Dujardin who plays the main role, decided not to attend the ceremony.
French culture minister Franck Riester said on France Info that a César for best director for Polanksi would be "a bad symbol" in terms of the awareness "we must all have in the fight against sexual and sexist violence".
Haenel had considered that "to distinguish Polanski is to spit in the face of all the victims".