Doug Martin carried the ball 22 times for 110 yards and a pair of scores for the Broncos (11-1, 6-1 MWC), as head coach Chris Petersen became the program's all-time leader in wins (72).
Tyler Shoemaker had seven receptions for 106 yards and a touchdown in the lopsided victory.
Boise State finished second in the Mountain West to TCU, which downed the Broncos 36-35 on November 12.
B.R. Holbrook threw for 145 yards for the Lobos (1-11, 1-6), while Crusoe Gongbay rushed for just 18 yards on seven carries to pace the team.
New Mexico has lost 21 straight on the road and finished 1-11 for the third consecutive season.