It was the second time in this three-game series Headley had been hit by a pitch and the third time it occurred in the last six games.
Headley remained in the game until the fifth inning when Alexi Amarista pinch-hit for him.
San Diego manager Bud Black said after the game that Headley should be fine for Friday's game against the Nationals.
"He's sore. He took one right in the back, sort of in the combo of Achilles and the low calf," said Padres manager Bud Black. "It just tightened up, it was sore, he wasn't moving good. He's had some calf issues. So we had to get him out of there.
Headley entered Wednesday's game hitting .199 with five home runs and 19 RBIs.
Corey Brock is a reporter for MLB.com. Keep track of @FollowThePadres on Twitter.Will Laws is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.