The Padres said in a statement Tuesday the 29-year-old Headley is expected to need four to six weeks for recovery.
Doctors Heinz Hoenecke, Daniel Keefe and Jan Fronek performed the operation at Scripps Clinic.
The Gold Glove third baseman was playing with knee pain since spring training.
Headley hit .250 with 13 homers and 13 RBIs this season, a major drop-off from last year when he finished fifth in the MVP voting. In 2012, he batted .286 with 31 homers and 115 RBIs.