Kelly left in the third inning of Tuesday night's game against the Orioles with stiffness in his right shoulder.
Interim manager Torey Lovullo said Wednesday ''It's probably not going to be the best thing to run him back out there.''
The move comes one day after the Red Sox shut down reliever Junichi Tazawa.
Lovullo says, ''Much like Taz, we just want to make sure our guys are healthy and ready for the next season.''
Kelly returned to Boston for an examination.
Kelly won eight consecutive starts before a no-decision on Tuesday. He is 10-6 with a 4.82 ERA in 25 games.