The 15-minute procedure, performed at Allegheny General Hospital by Dr. Patrick DeMeo, ends the season for the National League's defending batting champion.
The team noted on its Web site the surgery was designed to clean up the area around the shoulder cuff.
The injury bothered Sanchez for most of the last two seasons, despite cortisone shots.
"It kind of got worse the last couple of days," Sanchez said after Thursday’s game against Arizona. "This is something that got worse in the middle of the night."
"It was something that we anticipated having to get done at the end of the season that flared up more," said General Manager Neal Huntington. "There was no sense waiting any longer."
For the season, Sanchez hit .304 with 11 home runs and 81 RBI in 602 at-bats.