Bonser had the procedure Wednesday in St. Petersburg with Dr. Coco Eaton, who repaired the problems. The pitcher was bothered by tendinitis during the winter and when spring training started, persistent soreness and weakness in the joint prevented him from beginning his throwing program.
After two MRIs showed no structural damage, the exploratory surgery was recommended.
Bonser will need six to eight months to recover, leaving little room for him to return before the end of the 2009 season.
"Unless everything goes really, really well and ... miraculous," Twins manager Ron Gardenhire said.
After getting bumped from the rotation last year, the 27-year-old Bonser struggled in the bullpen for most of the summer before getting back on track in August. He finished 3-7 with a 5.93 ERA in 118 1/3 innings in 2008, but his powerful arm and big curveball made him the favorite for the long relief role this spring.
"He was in our plan," Gardenhire said. "We just have to make adjustments."
One or two spots in the bullpen are now open, depending on how many pitchers the Twins decide to take on the regular-season roster. R.A. Dickey, Phil Humber, Jason Jones and Jose Mijares will be looked at closely.