Edgar Gonzalez started at third base in place of Kouzmanoff on Tuesday, although Chase Headley figures to get the majority of starts there until Kouzmanoff returns to the lineup.
Headley, who had two hits Tuesday while playing left field, was in the starting lineup at third base on Wednesday.
"He's still a little sore but better than yesterday," Padres manager Bud Back said of Kouzmanoff. "He has limited mobility. It will take a few days for this to quiet down."
Kouzmanoff, who was walking gingerly in the Padres' clubhouse on Wednesday, said he was "leaning over [for a ground ball] and it locked up."
Kouzmanoff missed five games last season with a similar back injury. Oddly enough, it was Headley who was promoted from Double-A San Antonio to fill in for Kouzmanoff.
Paul McAnulty, who suffered a lower back sprain on Sunday in Cleveland, was back in the lineup for Wednesday's game. Outfielder Scott Hairston, who hyperextended his left elbow in batting practice on Saturday in Cleveland, is feeling "much better," according to Black.
Hairston took batting practice Tuesday and likely would have Wednesday had rain not canceled it at Yankee Stadium. He could possibly be in the lineup for the Interleague series finale on Thursday.
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.