"It got to a point where it was bothering me, and I didn't want to risk anything," he said. "I decided it was enough, to play it smart."
The move was precautionary, Peralta added, saying that he just didn't feel comfortable.
"Playing with a sore shoulder, I wasn't feeling comfortable and to do something wrong and get hurt is even worse," Peralta said.
With runners in scoring position and two outs in the sixth, it appeared Peralta would get a chance to add more damage to the D-backs 5-2 lead. However, Jon Jay pinch-hit for Peralta instead and struck out.
"He's been checked out by our medical team here," manager Torey Lovullo said. "We'll get him back tomorrow, see how feels and see what the next steps are."
No MRI was needed after the game, but Lovullo added that if Peralta feels discomfort on Monday, they'd reevaluate the situation.
"For right now, we're just going to see how he feels when he wakes up," Lovullo said.
Peralta started the game in left field, going 0-2 with a walk.
Kathryn Woo is a reporter for MLB.com based in San Diego.