"They're married and they're expecting their first child," their reps, Nicole King and Ken Sunshine, said in a statement.
The publicists did not reveal any additional details about the wedding, but the news follows weeks of marriage rumors, including claims that the pair would exchange vows in Garner's home state of West Virginia.
The couple met on the set of the 2003 comic-book movie Daredevil. They didn't begin dating until seven months after Affleck broke off his high-profile engagement to Jennifer Lopez, whom he was set to marry in September 2003.
"He's very happy," an Affleck friend told PEOPLE in April. "Jennifer is very down-to-earth, much more like him. They're more like-minded. That wasn't true (with Lopez)."
In early May, a close friend began spreading the news that the two were planning to wed, to the delight of Garner's parents. "They had their fingers crossed," a Garner pal told PEOPLE at the time. "They really love Ben." Soon after, she was sporting a diamond eternity band, though the couple kept mum about their plans. In late May sources said Garner was three months pregnant.
For Affleck, this is his first marriage. It's Garner's second marriage; she and actor Scott Foley divorced in 2003.
Meanwhile, Garner's Alias costar Ron Rifkin, appearing on Live with Regis and Kelly Thursday morning, said Garner's pregnancy will likely be worked into the show's storyline. "She's with child, and I think it's going to be written in," he said.