PEOPLE reports that the two met with a private judge at Garner's residence and signed all the paperwork necessary to make their divorce complete.
The couple began dating in 2004 and married in 2005. They have three children: 12-year-old Violet, 9-year-old Seraphina, and 6-year-old Samuel. Garner and Affleck announced their separation in 2015.
News of the separation comes just one day after Affleck released a statement about his recent stay in a rehabilitation facility where he sought treatment for substance abuse issues.
"This week I completed a forty day stay at a treatment center for alcohol addiction and remain in outpatient care," Affleck began his statement. "The support I have received from my family, colleagues and fans means more to me than I can say. It's given me the strength and support to speak about my illness with others."
"Battling any addiction is a lifelong and difficult struggle," the actor added. "Because of that, one is never really in or out of treatment. It is a full-time commitment. I am fighting for myself and my family."
"So many people have reached out on social media and spoken about their own journeys with addiction. To those people, I want to say thank you," Affleck went on to say. "Your strength is inspiring and is supporting me in ways I didn't think was possible. It helps to know I am not alone. As I've had to remind myself, if you have a problem, getting help is a sign of courage, not weakness or failure."
"With acceptance and humility, I continue to avail myself with the help of so many people and I am grateful to all those who are there for me," Affleck's statement concluded. "I hope down the road I can offer an example to others who are struggling."
Previously, Affleck's brother, Casey Affleck, commented on the Batman V. Superman star's decision to enter rehab in the first place, expressing support.
"Ben is an addict and an alcoholic. Most of my grandparents are alcoholics. My father is an alcoholic, as bad as you can be, and he's been sober for about 30 years," Casey said while speaking to Entertainment Tonight. "I've been sober for about six years. Ben is trying to put it together, and it can be a very hard thing to do. He has the kind of resources and time, luckily, to take the time and go to a good facility."
At this time, neither Affleck nor Garner appear to have released a statement on their divorce finalization.