Karnowski was scheduled to have surgery on Thursday afternoon. The news was first reported by the The Spokesman-Review.
"It was a tough deal, but needed to be done," coach Mark Few said. "It was actually getting progressively worse. I feel horrible for him -- he's such a good guy."
The 7-foot-1 native of Poland averaged 8.8 points and 5.4 rebounds over the first five games of the season but hasn't played since a 73-70 victory over UConn in the Bahamas on Nov. 27.
"The final decision for surgery wasn't made until this morning," a Gonzaga source told ESPN.
Karnowski could elect to receive a medical redshirt and play another season in college next year or could also decide to turn pro. A decision has not been made yet.
The loss certainly hurts Mark Few's program, but the Zags do have a couple of productive big men in Domantas Sabonis (17.5 points per game, 10.8 rebounds per game) and Kyle Wiltjer (20.2 PPG, 7.5 RPG) up front.
Gonzaga will face Santa Clara on the road on Thursday night.