Kirilloff, a 2016 first-round draft pick, will travel with Minnesota on its road trip to Los Angeles and undergo ulnar shortening surgery Tuesday.
"Any time you're talking about shaving a bone down or shortening a bone, I mean that's a substantial procedure," Twins manager Rocco Baldelli said. "But we're hopeful that by getting it done now gives us a chance to use the offseason to get right, to start swinging the bat again, to feel good and to start getting ready for next year."
It's the second time in Kirilloff's short career in the majors that he has had a season end early because of a wrist injury. A procedure last July on the same wrist ended his rookie season. He landed on the injured list twice this season, in April and June, because of issues with the wrist.
"As time went on, it just started to bother him more and more, to the point where we as a group were watching him hit in his final week of action and [it] didn't look like he could put the good swing on the ball that he can do," Baldelli said of Kirilloff, who was not made available to reporters.
Kirilloff, 24, has played 104 games in two years and batted .251 with 11 home runs and 55 RBIs.