Karnowski hit 7-of-8 free throws en route to 19 points and also grabbed 13 rebounds for the Bulldogs (9-1), who trailed 39-35 at halftime.
Kevin Pangos added 18 points and Gary Bell notched 15 points and nine rebounds. Gonzaga out-rebounded West Virginia (6-4) 43-36 with 31 of their boards coming on the defensive end.
Eron Harris led West Virginia with 23 points. Juwan Staten added 17. The Mountaineers lost for the third time in their last four games.