Mulroney, who cites "irreconcilable differences" as the reason for divorce, filed the papers June 8, People magazine reported.
It was revealed Monday that the couple had split in May 2005.
The court documents said Mulroney requested joint legal and physical custody of the couples' 7-year-old son Clyde Keener Mulroney and property rights will be determined by the court.
Mulroney stars alongside Lindsay Lohan in "Georgia Rule" and has also appeared in "My Best Friend's Wedding" and "Must Love Dogs."
Keener has been nominated twice for the Best Supporting Actress Oscar, in 2000 for "Being John Malkovich," and in 2006 for her character in "Capote." She also starred in "The 40-Year-Old Virgin."