Both cited irreconcilable differences as the reason for divorce, and they asked for joint legal and physical custody of their three children.
A representative for Affleck confirmed the news and described the relationship between Affleck and Garner as "very amicable."
The A-listers married on June 29, 2005. It is unclear when they actually separated, but their split was announced in June 2015.
“After much thought and careful consideration, we have made the difficult decision to divorce," they told People magazine in a 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. This will be our only comment on this private, family matter. Thank you for understanding.”
The couple continued to co-parent their children following the split, with Garner describing Affleck as the "love of her life" despite their split in an interview with Vanity Fair last year.
ABC News' Andrea Dresdale, Cleopatra Andreadis and Marilyn Heck contributed to this report.