The actors both filed divorce petitions in Los Angeles County Superior Court, citing irreconcilable differences and seeking joint custody of their three children, who range from 5 to 11.
The filings were made without attorneys and are virtually identical. Neither lists a date of separation.
The couple announced they were separating in June 2015 after 10 years of marriage.
“We go forward with love and friendship for one another and a commitment to co-parenting our children,” Garner and Affleck said in a joint statement at the time. “This will be our only comment on this private, family matter.”
The actors met while making 2003’s “Daredevil,” in which they both played superheroes.
Affleck, a two-time Oscar winner, announced last month that he had recently completed treatment for alcohol addiction.
His breakup from Garner returned him to the tabloids, where he had been a mainstay years earlier because of his relationship with singer Jennifer Lopez.
He lamented the renewed focus on his personal life after years of attention on his role as a parent, and the critical success of the Oscar-winning film “Argo,” which he produced and directed.
“This business tends to exaggerate highs and lows,” Affleck told The Associated Press. “I’ve had legitimate lows, movies I didn’t like, and I’m very proud of the movies I directed and so on. But you become a cast member in a soap opera that you’re not writing. You get the script every day and you find out what your role is that day.”