"In a way, it's a good thing," Stewart said by phone from Chicago on Monday. "It's a relief that something did show up."
The procedure will take place at the clinic in two phases, beginning with arthroscopic surgery.
When could Stewart return? Doctors said it might not be until early or middle September.
"You don't know if there's enough time [to play]," he said.
Stewart revealed he was going to have surgery late Sunday on his Twitter account, @Ian_Stewart_9. Asked by a fan when he was coming back to Wrigley, Stewart wrote, "Looks like next spring training, if the cubs bring me back."
Acquired from the Rockies for Tyler Colvin before the season began, Stewart batted .201 in 55 games with the Cubs, hitting five home runs. Could he be the Cubs' third baseman next season?
"He's got all the ability to do it," Cubs manager Dale Sveum said Monday. "I'd like to see some adjustment in the swing and stuff. Whether [the problem] was the hand or not, I think there still needs to be some adjustment. The defense is something you always want and the power and athleticism he brings. There just aren't that many around any more at third base who have those kind of attributes."
Stewart did have good batting-practice sessions but just couldn't replicate it in games.
"He'll even tell you the results have to start coming, whether it's something in the wrist or not," Sveum said. "This game is built on productivity, and you've got to produce to stay in the lineup."
Stewart's replacement at third, Luis Valbuena, was batting .226 in 16 games with three home runs. He was acquired off waivers from the Blue Jays on April 4.
"That was a heck of a pick by Theo [Epstein] on the last day of Spring Training," Sveum said of the acquisition by Epstein, the Cubs president of baseball operations. "He's a nice player to have in your organization for awhile. He can do a lot of things."