Black said Headley was unlikely to play in Wednesday's series finale against the D-backs. That, coupled with an off-day Thursday, could give him time to rest before the team opens a series on the road Friday against the Dodgers.
Headley started Tuesday's game and went 1-for-2 with an RBI single in the first inning. He was replaced by a pinch-hitter, Alexi Amarista, to begin the fifth.
"It started to spasm up on me after my second at-bat," Headley said, adding that the pain was in his lower right side.
"I can't imagine a scenario where I'll play tomorrow. But I don't necessarily think it's a strain."
Amarista remained in the game at third base for the Padres, who fell to the D-backs, 10-9, in 10 innings.
A year after leading the National League in RBIs, Headley entered the game hitting .239 with eight home runs and 35 RBIs.