Utah general manager Dennis Lindsey said various medical experts were unanimous in deciding surgery was the best option for Kanter's long-term health, decreasing the odds of another dislocation.
"Enes is disappointed. He's competitive, he's tough and he wanted to jump all in to the playoff race we're currently in," Lindsey said Tuesday before Utah's game against Oklahoma City. "Competitors, sometimes you've got to save them from themselves. ... and he plays such a physical style."
Surgery is set for Wednesday and will be performed in Chicago by Dr. Guido Marra. A timeline for his rehab will be determined after surgery, which will re-attach ligaments damaged by the dislocation.
The 20-year-old Kanter hinted last week that he might be done for the season when he indicated he was riding a stationary bike to stay in shape for "summer."
The injury occurred March 27 against Phoenix when 7-foot-2, 265-pound Suns center Hamed Haddadi fell on Kanter as they battled over a loose ball.
Kanter was averaging 7.2 points and 4.3 rebounds. The third overall pick of the 2011 draft had become a key part of Utah's rotation during the stretch run.
The Jazz entered Tuesday's game trying to hold on to the eighth playoff spot in the Western Conference.
They also will be without guard Alec Burks (sprained ankle) and forward Marvin Williams (stomach flu).