Pedroia missed 44 games after he broke a bone in his left foot on June 25 at San Francisco.
He returned to the lineup on Tuesday and played in back-to-back games, but did not play on Thursday because of pain in the foot, which became more pronounced on Friday.
"I'm going back on the DL. I'm not feeling very good," Pedroia told reporters on Friday. "I played those two games and tried to do it, and then yesterday I couldn't do much and then today was a lot worse.
"They're backing me off and not letting me do anything."
The Red Sox fear that although Pedroia's foot has healed since the original injury, it is not completely healed and that he could do further damage by attempting to play.
"They did a scan, and while it showed really good healing, it also showed that there's still probably some healing to go," Red Sox manager Terry Francona said.
"I think the layman's version is that they tried to impress upon him a lot that if it hurt, you better tell us, because then you're going to hurt yourself.
"He did that, and we give him some credit."
(Reporting by Mike Mouat in Windsor, Ontario; Editing by Greg Stutchbury)