Gonzaga (28-6) raced out to a 21-point lead in the first half and had an answer when BYU fought back in the second half, leaving no doubt about the NCAA tournament by earning the conference's automatic bid.
Gary Bell Jr. had 14 points and David Stockton dished out seven assists to send the Bulldogs to the NCAA tournament for the 16th straight year.
BYU (23-11) rallied after a dismal first half, pulling within eight with 3 minutes left. The Cougars couldn't finish off the comeback and now have a long five-day wait until Selection Sunday.
Tyler Haws had 24 points and Kyle Collinsworth added 13 before leaving with a right leg injury in the second half.
Gonzaga and BYU split two meetings during the regular season.
The Zags won the first one by 15 after hitting 10 of 22 3-pointers in Spokane. The Cougars were much better guarding the perimeter in Provo, limiting the Bulldogs to 4 of 18 shooting from 3-point range.
Playing in its 17th straight WCC final, Gonzaga dominated early in the rubber match with a nearly perfect first half.
Offensively, the Bulldogs built a quick nine-point lead and kept pouring it on behind Dower, who had 14 points on 7-of-11 shooting in the first half.
Gonzaga was just as good defensively, contesting shots inside and getting out to BYU's shooters on the perimeter. The Cougars struggled against the Bulldogs' pressure, missing 11 of their first 15 shots on their way to a 9-for-27 half.
Gonzaga led by as much as 21 in the first half and was up 44-27 at the break.
The Bulldogs didn't let up, either, thanks to Dower.
The athletic left-hander scored on a hard drive and was fouled, then threw down a pair of dunks to put the Bulldogs up 53-33.
BYU suffered another blow when Collinsworth had to be helped off the court midway through the second half, unable to put any weight on his right leg after going down under Gonzaga's basket.
Playing without its facilitator and second-leading scorer, the Cougars found a way to claw their way back.
Haws has had trouble getting shots to fall in the WCC tournament and had a so-so first half, scoring nine points on 2-of-7 shooting. When his shots started to fall in the second half, so did Gonzaga's lead.
Haws hit a 3-pointer in rhythm to cut Gonzaga's lead to 13 and the Cougars kept chipping away at the lead, getting it down to eight on two free throws by Haws with 2:56 left.
That was it for BYU, though, leaving the Cougars to wait to see if the selection committee believes their resume is good enough for an NCAA tournament bid.