The Spider-Man actor and Jennifer Meyer - who already have a two-year-old daughter Ruby Sweetheart - welcomed their new arrival into the world on Friday.
Tobey's representative said: "I can confirm the Maguires had a baby boy and the family is healthy and happy."
No further details about the birth or the baby, including his name, are yet to be released.
Tobey, 33, and 32-year-old Jennifer met in 2003 and married in Hawaii in September 2007.
Earlier this year, Tobey revealed daughter Ruby was thrilled about becoming a big sister and was amazed by how much her mother Jennifer's stomach was growing.
He said at the time: "Ruby is loving it. She's really into the belly and how it is growing. Ruby's not really jealous, she just loves being around people, and this will be like having another little playmate."
News of the pregnancy broke last year, with a source saying in November: "They are both thrilled to be becoming parents again. They can't wait to expand their family with another little one."