"He's got some flu-like symptoms going on. Felt it during the game [Saturday night], overnight," Farrell said. "It worsened to the point where he can't go today, at all.
"He's been seen by our doctors, antibiotics administered. So hopefully this is a short-lived situation."
Pedroia exited Friday night's game in the ninth inning with discomfort in his right foot. He fouled a ball off his foot in the third, but scans came back negative and he was in the lineup Saturday.
Pedroia has played in all but four games this season, including Sunday's. He's batting .284/.345/.379, and according to Fangraphs, leads the Red Sox in wins above replacement with 3.7.
Steven Petrella is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.