Bulldogs coach Mark Few said Karnowski had surgery on Thursday.
The 7-foot-1 center has been out since Nov. 27 due to a bulging disc and has missed six games. He averaged 8.8 points and 5.4 rebounds in five games.
Karnowski has been one of college basketball's best big men the past three seasons, causing matchup problems with his size and footwork, while anchoring Gonzaga's defense.
The Zags (11-3, 1-0 West Coast) opened the season No. 9 in The Associated Press Top 25, but dropped out of the poll in mid-December after two losses in three games.
Karnowski, a senior, could be eligible for a medical redshirt since he played in just five games.