A screw was inserted into the foot in Friday's operation. The 2008 AL MVP finished the season with 12 homers, 41 RBIs and a .288 batting average.
Pedroia fouled a ball off his foot on June 25. He was sidelined until Aug. 17 and played in just two games before pain in his foot sent him back to the disabled list.
Pedroia said before Thursday's game in Baltimore, where Boston wrapped up a three-game series, that the operation would help the foot heal.
The injury limited him to 75 games this season after he averaged 150 the past three seasons.