After failing to score in the first half, the Cougars scored on their second play of the second half, as Jamaal Williams sprinted 66 yards untouched to make it 7-7 just seconds into the third quarter.
But Nevada answered quickly.
The Wolf Pack took a 14-7 lead with an 11-play, 75-yard drive. Nevada punted on 4th-and-inches, but a BYU player was penalized for attempting to leap over the protective shield in front of the punter, and the Wolf Pack had new life at midfield.
The Cougars then mounted a nine-play, 80-yard touchdown drive to tie it again, this time at 14-14. Taysom Hill's 10-yard strike to Kaneakua Friel produced the touchdown.
After a big defensive stop, the Cougars put together another decent drive, and found the end zone when Hill threw a 3-yard touchdown pass to JD Falslev with 14:50 remaining in the fourth quarter to give BYU a 21-14 lead.
Aided by a defensive pass interference penalty on third down, Nevada cut into the lead with a 70-yard drive. Brent Zuzo's 24-yard field goal trimmed BYU's lead to 21-17 with 9:02 left in the game.
The Cougars then seemingly wrapped it up with an eight-play, 75-yard touchdown drive, capped by Hill's 35-yard run on third-and-10. The TD made it 28-17 with 6:40 remaining.
Nevada scored with 2:42 remaining on a 4-yard pass from Fajardo to Brandon Wimberly, but Kyle Van Noy intercepted the two-point conversion attempt.
Fears that the Cougars would show up flat and uninspired were realized in the first half.
Nevada took a 7-0 lead at halftime, after the Cougars shot themselves in the foot in the first half with mistakes and costly penalties.
BYU was penalized 10 times for 87 yards in the first half and generated just 150 yards of offense against a team that was yielding 500 yards per game.
The Wolf Pack drove 81 yards on just eight plays to score on their first possession. A 30-yard run by Brock Kendall and a 27-yard flea-flicker to Brandon Wimberly set up Kendall's 2-yard plunge.
The Cougars moved into Nevada territory just once in the first quarter, but went away with nothing after a 4th-and-7 run from the 32 was snuffed by the Wolf Pack defense.
Early in the second quarter, Robertson Daniel intercepted a pass in the end zone, snuffing a promising Nevada drive.
Holding penalties thwarted three BYU possessions in the first half, and a turnover stopped one from even getting started.
BYU's Logan Taele blocked a field goal in the first quarter after Cody Hoffman fumbled a punt deep in BYU territory.