People reported the 46-year-old actor entered a treatment facility Wednesday and is seeking help for substance abuse issues.
"He knew he needed help and was vocal about it," a source said.
Garner visited Affleck at home Wednesday and was "visibly upset" as she left the house. She returned with an unidentified woman and was spotted driving the woman and Affleck away in a car.
TMZ said Garner, Affleck and the woman stopped at a Jack in the Box before heading to a rehab facility in Los Angeles County.
Affleck previously sought treatment in 2001 and in December. He was spotted receiving an alcohol delivery outside his home Monday.
Affleck and Garner split in June 2015 after 10 years of marriage. The pair are parents to three children: 12-year-old daughter Violet, 9-year-old daughter Seraphina and 6-year-old son Samuel.