The actors, who already have 5-year-old Violet and 2-year-old Seraphina Rose together, released a short statement saying that they are "thrilled" at the prospect of becoming parents again.
A spokesperson for Garner denied rumors that she was expecting in May, after the former Alias star was photographed wearing baggy clothes on numerous occasions.
Garner also slammed baby reports in June 2010, with her representative saying at the time: "Jennifer is absolutely not pregnant."
The couple met on the set of 2004 movie Daredevil and married in 2005. Garner later admitted that Affleck won her over with "persuasive" emails.
She has previously said of her husband: "Ben is sexy and kind, but he's also a riot. We can be very goofy together. He doesn't have trouble wiggling his way in anywhere. Ben is charm personified when he wants to be.
"He's not easily threatened or made uncomfortable - he's very secure in that way. Maybe he just knows I'm nuts about him, and he doesn't have anything to worry about."