Zimmerman was in the starting lineup for both games of the doubleheader against the Dodgers.
Manager Davey Johnson then announced that Zimmerman will have minor surgery after the season. Zimmerman is expected to be ready for Spring Training.
"It's probably a cleanup. In this day and time, it's not a big deal," Johnson said. "He is going to have some treatment by [team medical director] Dr. Wiemi [Douoguih] prior to the game. It's not nearly as bad, but it has been acting up lately."
Zimmerman's shoulder has given him problems since early April. He landed on the 15-day disabled list because of shoulder inflammation and returned to action in early May.
The injury has not stopped him from having a solid season. Entering Wednesday, Zimmerman was hitting .284 with 22 home runs and 84 RBIs.
"He is playing great as far as I'm concerned," Johnson said. "The results from the [last cortisone shot was] so good and he felt so much better."