The Broncos (5-0) got off to a slow start and struggled to run the ball against the FCS Aggies.
The Broncos rushed for just 101 yards, far below the 214 yards per game they were averaging. Boise State got just 13 points in four trips to the red zone in the first half before Moore finally helped the offense get on track in the second half.
Moore was 22 of 31 with one interception. His longest TD pass was 42 yards to Titus Young. Pettis had 10 catches for 129 yards, while Young had six catches for 83 yards.
Doug Martin added a 4-yard TD run in the final minute of the game to close out the scoring.
The Aggies (1-3) were led by quarterback Greg Denham, who was 24-of-36 for 206 yards and two touchdowns.