Pedroia's wife, Kelly, delivered the couple's second son.
When Kelly Pedroia went into labor on Wednesday, Pedroia left Fenway Park after the sixth inning.
Prior to Thursday's game, Red Sox manager Bobby Valentine wasn't sure if Pedroia would fly with the team to Toronto for a three-game weekend series.
"The only thing I can tell you about Dustin is that we've heard that everybody is doing fine, and that's really good news," Valentine said.
In past generations, it wasn't accepted for players to leave their team for the birth of a child. But it has now become commonplace, something Valentine appreciates.
"It's a change, and I think the family is the No. 1 importance in everyone's life," Valentine said.
Pedroia has been on fire for the Red Sox since Aug. 5, batting .381. In that span, he's raised his average from .262 to .295.