Nevada (7-4) trailed the Dons 27-26 at halftime, but after Malik Story made a lay-up to give the Wolf Pack a 28-27 lead just 1:29 into the second half, Nevada never trailed again.
The Wolf Pack led by as many as 15 in the second half, but San Francisco (5-3) cut Nevada's lead to two after Cody Doolin hit a pair of free throws to make it 51-49 with 2:41 to play.
Nevada was 17 of 24 from the free-throw line, out-rebounded the Dons 45-30 and forced San Francisco to turn the ball over 18 times.
Cole Dickerson scored 11 points and had nine rebounds for San Francisco. Tim Derksen and Tao Xu each had 10 points.