The pair, both 44, filed a petition together after 10 years of marriage.
The couple had previously announced in 2015 that they were splitting.
"After much thought and careful consideration, we have made the difficult decision to divorce," they said in a joint statement at the time. "We go forward with love and friendship for one another and a commitment to co-parenting our children whose privacy we ask to be respected during this difficult time."
In court documents, the pair said they want joint legal and physical custody of their three children -- two daughters, 11-year-old Violet and 8-year-old Seraphina, and a 5-year-old son, Samuel.
They began dating in 2004 after working together on Pearl Harbor (2001) and Daredevil (2003), and married in 2005.
News of the filing comes a month after the actor revealed on Facebook that he had completed a stint in rehab.