The actor, 40, filed for divorce in January from the British model, 31, reported People magazine.
He listed "irreconcilable differences" on the divorce papers. The documents list the date of separation as December 28, 2014.
The couple wed in June 2012 after a very quiet courtship. It was Deyn's first marriage and Ribisi's second. They had no children together. The 'Selma' actor has a daughter, Lucia, 17, from his marriage to Mariah O'Brien, which ended in 2001.