Derrick Marks scored 16 points on 11-of-11 shooting from the free throw line and Ryan Watkins finished with 15 points and 10 rebounds for the Broncos (21-12), who will face New Mexico in the semifinals on Friday.
Deonte Burton scored 22 points and Cole Huff added 17 points for the Wolf Pack (15-17), who shot just 32.1 percent from the field.
Nevada led 57-56 after a Huff 3-pointer and a Michael Perez layup with six minutes left, but a 9-0 burst put Boise State in front for good.
Boise was 10-for-10 from the free throw line down the stretch to seal the win.
The teams went into the break locked in a 32-32 tie.