The team said the 34-year-old right-hander had the procedure Monday.
Phelps last pitched May 2 against Atlanta. Three days later, he felt uncomfortable while warming up against Oakland and was replaced by Tyler Chatwood. Toronto said at the time that Phelps had discomfort in his pitching shoulder and later sent him for an MRI.
"He was awesome for the bullpen. He was awesome for the young guys and we're going to miss him a lot," manager Charlie Montoyo said. "He was probably one of our best relievers, and what he did in the clubhouse was awesome, too."
Phelps is 34-38 with a 3.90 ERA and six saves in nine major league seasons with the Yankees (2012-14), Marlins (2015-17), Mariners (2017), Blue Jays (2019, '21), Cubs (2019), Brewers (2020) and Phillies (2020). He returned to the Blue Jays this year for a $1.75 million, one-year contract.
Phelps missed the 2018 season after getting hurt during spring training and having Tommy John surgery.