Pedroia came out of Wednesday night's loss to the Yankees after 1½ innings and was examined in New York rather than traveling with the team to Tampa Bay.
Pedroia, 35, missed all but three games last season while rehabbing the knee after having cartilage restoration surgery following the 2017 season.
"He felt a pop, I think he said, yesterday," Dave Dombrowski, the team's president of baseball operations, said on WEEI radio Thursday. "As we know, the knee is never going to be 100 percent. It's amazing that any player can play with what he's gone through."
Pedroia began the season on the injured list with left knee inflammation. He was activated April 9 for the Red Sox's first homestand and is 2-for-20 at the plate.
The Red Sox called up right-handed pitcher Marcus Walden from Triple-A Pawtucket to take Pedroia's place on the roster.
The reeling Red Sox, 6-13 after a two-game sweep by the Yankees, open a three-game series against the East-leading Tampa Bay Rays at Tropicana Field on Friday.