The Rosemary's Baby filmmaker, who lives in France, was due to collect the award in 2009 when he was taken into custody by airport officials in Zurich more than 30 years after he fled America and skipped sentencing on a charge of unlawful sex with a minor.
He subsequently fought extradition to the U.S. and was allowed to walk free in 2010, following several months of jail time and house arrest at his Swiss chalet, after officials rejected the extradition bid.
The 78 year old returned to the film festival on Tuesday to accept the top award.
Polanski told cheering audience members, "What can I say? Better late than never. It's a very moving moment for me. It's a strange anniversary for me - two years, day for day."
Speaking about his arrest, he added, "Certain parts of it I'd rather forget, but I'm happy to be here. It was not only a blow to me, but also to my family and the festival itself. I would in particular like to thank the prison staff who tried to make my stay as bearable as possible, including the head of the prison of Zurich."
He also debuted a documentary, Roman Polanski: A Film Memoir, which chronicles his side of the arrest saga as well as his career and personal life.