Polanski, whose film "The Ghost Writer," debuted at the festival, was unable to attend the ceremony, as he remains under house arrest in his Swiss chalet in Gstaad.
Producer Alain Sarde, who accepted the prize on Polanski's behalf, said the director told him he would not have attended the festival even if he had been free, "because the last time I traveled to accept an award I landed in jail."
Polanski was arrested when he arrived in Zurich on Sept. 26 to receive a lifetime achievement award from a film festival. The Swiss must decide whether to extradite him to the U.S. to face possible further sentencing in a 32-year-old sex case.
A joint Silver Bear for best actor was awarded to the stars of the Russian film, "How I Ended the Summer." Grigory Dobrygin and Sergy Puskpalis played opposite one another as an older and younger researcher who clash at a polar station on an island in the Arctic Circle.
Shinobu Terajima won the best actress for starring as a wife forced to tolerate the tyranny of her husband who returns disabled from the second Chinese-Japanese war in the Japanese film "Caterpillar."
A Romanian film, "If I Want to Whistle, I Whistle" by Florin Serban of Romania was awarded the Silver Bear runner-up prize. It depicts the tough story of a youth who panics that his mother will flee the country with his younger brother while he is in a juvenile reform center.
The winning film, "Honey," tells the story of a 6-year-old boy who stops speaking when his father disappears. It was filmed in the lush mountains of the Turkish countryside where the boy goes in search of his father, a beekeeper.
Director Semih Kaplanoglu said the award was "like a rebirth" and he hoped that it would be an inspiration to young filmmakers in Turkey.
"The Ghost Writer," based on a novel by Robert Harris, stars Pierce Brosnan as a former British prime minister, Olivia Williams as his wife and Ewan McGregor as a ghost writer hired to complete his memoirs on a rain-swept island off the U.S. east coast.
The movie, Polanski's first since "Oliver Twist" in 2005, was nearly complete at the time of his arrest.