The veteran first baseman will have the procedure performed later this week to repair the cartilage and will require a two-month rehab, but he's expected to make a full recovery before Spring Training.
"It's not a good feeling to have surgery, but I'm happy to get it done, because it has been bothering me a lot every swing I make," Encarnacion said. "I just want to get it done.
"The last couple of weeks were worse. Every swing I make I've been feeling it, so I can't swing it like that anymore."
The Blue Jays have known for the past couple of weeks that surgery would be required, but Encarnacion was allowed to continue playing because it was determined he couldn't do any further damage to the area.
Encarnacion wanted to finish the year but decided to step aside when the pain became too much. That moved up the timeline for his surgery, but it remains the exact same procedure that was going to be performed in the first place and the injury isn't considered as serious as the one Jose Bautista suffered last year.
The 30-year-old Encarnacion now has his season come to a close just four home runs shy of 40. He was looking to become just the third player in franchise history to hit that 40-homer milestone in back-to-back seasons after Bautista and Carlos Delgado previously accomplished the feat.
"That was my goal, I tried to finish the year playing with the team and I tried to make it to 40 home runs," Encarnacion said. "I wanted to try to make it two years in a row, but the way I was feeling, I couldn't make it. But I feel good with my season and I hope next year we come back playing better, and for this time in the year, next year, to be playing for the playoffs."
Encarnacion arguably was the Blue Jays' most valuable player again this season. He hit .272 with an impressive .904 OPS while driving in 104 runs in 142 games. The numbers were eerily similar to last season during a breakout year that resulted in a lucrative multi-year contract extension.
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.