Alonso returned from the disabled list on July 26 after missing 30 games with tendinitis in his right wrist. He was hitting .421 (16-for-38) since returning.
Alonso wasn't available for comment after the game as he was getting an MRI.
"That was a weird one," said Padres manager Bud Black. "He was standing right next to me and had a bat in his right hand. He did something with the bat that triggered some discomfort."
Black indicated that the pain was in the same area where Alonso has previously had issues this season.
The Padres moved Tommy Medica from left field to first base after Alonso left the game, and then sent third baseman Yangervis Solarte to left field. Chris Nelson came off the bench to play third base.
Corey Brock is a reporter for MLB.com. Keep track of @FollowThePadres on Twitter. This story was not subject to the approval of Major League Baseball or its clubs.