Polanski, 76, missed out on the world premiere of his film at the Berlinale, the first major international cinema showcase of the year, due to his house arrest in Switzerland for having sex with a 13-year-old American girl in 1977.
The Silver Bear trophy was accepted by a producer of the film, Alain Sarde.
“I am sure Roman will be very happy,” he said.
“However, when I was lamenting with him that he cannot be with us, he said to me, ‘Even if I could, I wouldn’t because the last time I went to a festival to get a prize, I ended up in jail’,” he quipped.
Benmussa was referring to the director’s arrest in September on a US warrant when he went to Zurich to accept an award.
A seven-member jury led by German director Werner Herzog (Fitzcarraldo) and including Oscar-winning actress Renee Zellweger gave top honours to Turkish film Honey starring a seven-year-old boy.
The picture tells the story of a struggling pupil who loses his father in a freak accident.
It is the third in a trilogy by director Semih Kaplanoglu tracing the life of Yusuf and his development as an artist and human being in rural Turkey, played here by now eight-year-old Bora Altas.
The stars of the Russian drama How I Ended This Summer, Grigori Dobrygin and Sergei Puskepalis, shared the Silver Bear on Saturday for best actor.
How I Ended This Summer is the second solo feature film for Russia’s Alexej Popogrebski, 37, about an experienced meteorologist and an intern working at a remote polar station.
Japan’s Shinobu Terajima won the Silver Bear for best actress for her role in the harrowing anti-war drama Caterpillar as the long-suffering wife of a severely disabled World War II veteran.
Critics had showered The Ghost Writer with praise after its premiere, calling it a return to form for the French-Polish film-maker, best known for classics such as Rosemary’s Baby and Chinatown.
New York Times critic Manohla Dargis gave the film a glowing review.
“Mr Polanski is a master of menace,” he said.
“He creates a wholly believable world rich in strange contradictions and ominous implications.
“He’s delivering the pulpy fun at such a high level that The Ghost Writer is irresistible, no matter now obvious the twists.”
The picture, based on Robert Harris’ best-seller The Ghost, features a stand-out performance by Pierce Brosnan as a former British prime minister modelled on Tony Blair being probed for war crimes over the torture of terror suspects.
He hires a ghost writer (Ewan McGregor) to shape up his memoirs but the hired scribe soon stumbles upon a deadly web of transatlantic political intrigue.