The teams combined for 800 yards of offense despite playing in a constant rain.
The Broncos captured the Western Athletic Conference title and ended their regular season with a 12-0 record. They must now wait to see if they will receive a berth to play in a BCS bowl. Nevada closed its regular season at 8-4.
Boise State held a 27-3 lead midway through the second period, but the Wolf Pack twice closed the deficit to eight in the second half.
A 71-yard scoring run by Nevada's Vai Taua cut the Boise State lead to 34-26 and the Wolf Pack regained the ball with 13:25 remaining in the game. Taua, however, fumbled the ball away at his own 32-yard line and the Broncos quickly drove to a 27-yard field goal by Kyle Brotzman.
Moore then threw his fifth touchdown pass with 5:08 to play -- a 60-yarder to Kirby Moore that made it 44-26.
Nevada added a score with 1:25 left on the third touchdown pass of the night by Colin Kaepernick.
Three of Moore's scoring passes went to Don Paul, all coming in the first half. Moore completed 17-of-33 passes for 253 yards without an interception.