Pedroia was set to bat second when the Red Sox played at Toronto.
The 2008 AL MVP was in Boston on Thursday while the Red Sox were in New York, beating the Yankees 8-3.
The Red Sox team doctor said Pedroia had a bruised kneecap. Pedroia also said there was a small piece of loose cartilage.
Pedroia and Boston manager Terry Francona said the injury isn't likely to get any worse if he keeps playing.
"I kind of lucked out. It's just a bruise," Pedroia said. "It's been bugging me for a while. So as long as I can continue to play and just deal with it, it feels good, I guess."
The 27-year-old Pedroia is hitting .247 this season.
"I think yesterday was important because I think he'll relax a little bit more now," Francona said. "I'm sure he has pain in his knee but now he knows he's not going to hurt himself."
The Red Sox also recalled right-hander Michael Bowden from Triple-A Pawtucket on Friday and optioned catcher Luis Exposito to the minor league team.