A source told the magazine the baby was born in Santa Monica, Calif.
The new addition joins the couple's two daughters, Violet, 6, and Serafina, 3.
Garner, 39, announced her pregnancy in August, saying she would be thrilled to have another girl. And she said Affleck, 39, was excited no matter what the gender.
"I would have thought [he wanted a boy]. At first ... I really thought so," Garner told Jay Leno in January.
"And then [Ben] kind of said, 'Well, we have girls. We know how to do girls. My girls love me. I'm the big guy in the house.' So, now I'm not sure."
The couple met after starring together in "Daredevil," and married in June 2005.