"Jen is feeling good," a source tells PEOPLE. "She's so thrilled to have a little boy, and the girls already love him so much."
Their son Samuel joins big sisters Seraphina, 3, and Violet, 6.
While the actress told Ellen DeGeneres that "it would be so weird to have a boy," Garner seems to be taking it all in stride.
"Jen is such a natural mother," says a source close to the couple.
The proud parents, both 39, have always put family first.
"He couldn't be happier," Affleck's friend tells PEOPLE. "He loves his wife. He loves his family and he's proud – he's legitimately proud – you can just see it."
As for Affleck, who has been acting less to focus on directing lately, his most important role is being a father.
"He's gets to spend a lot of time with his family and the idea that they have three kids right now is something that makes them both feel really good," the source adds.
The couple, who wed in June 2005, announced they were expecting their third child in August.
For more on Affleck and Garner's growing family, pick up the latest issue of PEOPLE, on newsstands Friday
With reporting by Elizabeth Leonard and Liz McNeil