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The couple has not yet announced the name of their son.
Tobey, 33, and Jennifer, 31, welcomed their first child – Ruby Sweetheart – in November 2006.
And earlier this year, Tobey said Ruby was very excited about her mom being pregnant.
"She's loving it. She's really into the belly and it growing and her baby dolls," Tobey told E! News. "Ruby's not really jealous. She just loves being around people, and this will be like having another little playmate."
Tobey and Jennifer, a jewelry designer, married in September 2007 in a ceremony in Hawaii.