The 30-year-old will have the surgery performed by Dr. James Andrews on Aug. 19. There's a chance he could return at some point late next year but will face an uphill battle to get back to the big leagues before 2016.
Wagner last pitched for the Blue Jays on May 14 when he threw 46 pitches over 1 1/3 innings in a lopsided loss to the Indians. He was optioned to the Minor Leagues after the game and made four appearances with Buffalo before he was shut down.
The native of Minnesota was an intergral part of the Blue Jays bullpen in 2013. He posted a 3.79 ERA with 33 strikeouts over 38 innings but lost his spot on the roster this year because he had Minor League options remaining and other relievers did not.
Gregor Chisholm is a reporter for MLB.com. Read his blog, North of the Border, and follow him on Twitter @gregorMLB. This story was not subject to the approval of Major League Baseball or its clubs.