Publicist Karen Samfilippo confirmed the filing Monday in Los Angeles Superior Court but declined to comment.
The couple were married about three years and separated in October. This is the second divorce for the actress, who was previously married to former baseball outfielder David Justice.
Tabloids speculated about Benet's faithfulness from nearly the moment the "X-Men" star married the singer in January 2001.
The two met in 1999 at a party to celebrate the premiere of Berry's HBO movie "Introducing Dorothy Dandridge," about the first black woman nominated for a best-actress Oscar with 1954's "Carmen Jones."
Berry won a Golden Globe and an Emmy for the Dandridge role. She then became the first black woman to win a best-actress Oscar for her work in 2001's "Monster's Ball."
Benet has a young daughter, India, from a previous relationship with a girlfriend who was killed in car crash 15 months after the girl was born.
His first album, "True to Myself," was released in 1996. He has had such hits as "Spend My Life With You" and "Love Don't Love Me."