Air Force's loss left Utah as the only Mountain West team undefeated in conference play.
Van Pelt's versatility helped the Rams (5-3, 2-1 Mountain West) generate 564 total yards and moved the defending champions back into contention in the conference.
Air Force (6-2, 3-1) was led by quarterback Chance Harridge, who ran for 136 yards and two scores. He was intercepted twice, both times by safety Benny Mastropaolo.
Van Pelt ran for 125 yards and completed 14 of 22 passes for 258 yards. David Anderson caught nine passes for 199 yards -- both career highs -- including a 5-yard scoring pass.
After a scoreless first quarter that included Air Force's block of a Colorado State field goal attempt, the teams combined for 37 points in a wild second quarter, with CSU leading 23-14.
Van Pelt got it started, capping an 89-yard drive with a 13-yard scramble barely three minutes into the period.
Pass plays -- a rarity in Air Force's wishbone offense -- played key roles in the Falcons' two scores in the quarter. Matt Ward turned a screen pass into a 32-yard gain, and Harridge hit Joe Schieffer on a 41-yard pass on the next play, setting up Harridge's 1-yard scoring run.
After Colorado State's Jeff Babcock kicked a 48-yard field goal, equalling his career longest, Air Force got a quick score when halfback Schieffer took a pitchout and heaved a 69-yard scoring pass to a wide open Alec Messerall for a 14-10 lead.
Van Pelt put the Rams back in front, culminating a 65-yard drive with a 3-yard scoring run.
Van Pelt's 38-yard pass to Anderson set up another Colorado State score with 1:01 left in the half. Van Pelt faked to his tailback going right, then found Anderson wide open on the left side of the end zone for a 5-yard score.
Anderson had six catches for 148 yards in the half, including receptions of 31, 36 and 38 yards.
Marcus Houston's 12-yard run put Colorado State ahead 30-14 late in the third period.
Air Force responded with a 15-play, 80-yard drive that ended on Harridge's 2-yard TD run, but a pass on the 2-point conversion attempt fell incomplete.