Pedroia, 33, was hurt in the first inning after falling over Jose Abreu while running to first base. Josh Rutledge took over at second base.
After the game, Red Sox general manager Dave Dombrowski told reporters Pedroia's X-rays were negative, but that he will travel back to Boston for an MRI.
The former AL MVP was uncharacteristically healthy last season, playing in 154 games. He had missed 96 games the previous two seasons and has been held out in 20-plus contests in three of the past five years. A healthy Pedroia led to a return to form, as he posted 5.2 wins above replacement (FanGraphs formula) and hit 15 home runs for the first time since 2012.
The Red Sox have also passed the leadership mantle to Pedroia from David Ortiz this season.
"I don't want to say it's de facto or an assumption that Dustin becomes that guy," manager John Farrell told reporters. "He's the elder statesman, the longest-standing player here. He's been a leader in his own right and will continue to be that.
"...I think eyes will go to Pedey, for one who has been a champion here multiple times, has experienced so many different sides of baseball in Boston, that he'll be a steady force for a lot of our young players."
The Red Sox will hope whatever is ailing Pedroia proves minor, as they look to contend for a World Series championship.