Headley was injured in the batting cage before Tuesday night's game against the Rockies, according to Padres manager Bud Black. Headley went 0 for 4, dropping his average to .160 with one homer and four RBIs.
Headley was slowed by a strained right calf during spring training and missed the first 14 games last season because of a fractured left thumb. He led the NL with 115 RBIs in 2012.
Alexi Amarista started at third base in place of Headley. San Diego's Yonder Alonso, usually a first baseman. took ground balls at third base before the game.