Pedroia felt a pinch in his side while swinging the bat in warmups on Saturday before Team USA faced Puerto Rico in second-round action in the Classic. He was replaced on the roster by Baltimore's Brian Roberts.
Mark DeRosa played second base on Saturday night.
In first-round pool play in the Classic, Pedroia was 2-for-16 with a pair of doubles.
"I was hitting extra [Saturday], and I kind of felt a little soreness," Pedroia said. "I started taking flips today. I kind of felt a shooting pain, a little bit."
Hitting coach Reggie Smith immediately shut Pedroia down once he said there was discomfort.
The All-Star second baseman has been in contact with the Red Sox, and he left Miami for Fort Myers late Saturday afternoon. He didn't stay for Team USA's game with Puerto Rico at Dolphin Stadium.
In preparation for the Classic, Pedroia did some extra training in the offseason. From the first game of the Classic in Toronto, he played all nine innings.
Pedroia said he has never had an oblique issue.
"No. Nothing like that. I've never really had anything like this," Pedroia said. "It's frustrating. Obviously I trained really hard in the offseason to prevent something like this from happening. Maybe I pushed it a little too hard, too fast to get this going. I'll get this checked out Sunday."
The timing of the ailment comes about three weeks before Opening Day, but the All-Star second baseman fully expects to be ready by them.
"I'll be fine. I'm not concerned about the season," Pedroia said. "I'll be ready for the season. I'm not worried about that."
Known as a gamer who plays all-out, Pedroia is disappointed leaving his team during the second round. When he left the ballpark, he was hopeful he might be able to return.
"I'm not too excited about leaving," he said. "This is a great time, obviously, representing your country. This is the second round, and games are going to get extremely exciting and fun. Hopefully, everything checks out good [Sunday] and I'm back."