Santos was shut down in April because of inflammation in his right shoulder. He attempted to rehab the injury but the pain never went away.
Toronto's Opening Day closer will now begin post-surgery rehab in 10 days after the procedure went well and didn't reveal any additional damage.
"Some wear and tear in the joint, no specific tears of any kind," Blue Jays manager John Farrell said of the surgery, which was centered around the labrum. "So, it was a general cleanout, and based on his findings, probably the best-case scenario given surgery was required."
Toronto typically has its pitchers begin their offseason throwing program in early-to-mid December. Santos is expected to be recovered by then and shouldn't have any problems getting ready for the start of the season.
The Blue Jays feared a more serious problem could be found during the medical procedure. The fact that there was only some fraying around the labrum and not a tear means Santos should be able to avoid another long-term setback.
"You're always waiting with anticipation to find out truly what's going on there and you don't know until they go in there with a scope," Farrell said. "I think in this case, Sergio got the best news that he could have under the circumstances."
Santos was acquired from the White Sox in an offseason deal for prospect Nestor Molina. Santos appeared in just six games for the Blue Jays this season and allowed five runs in five innings with two saves.