The Bulldogs broke open what had been a tie game midway through the first half to take a 39-21 advantage at the break.
Dower made all seven of his field goal attempts while Kevin Pangos had 14 points and Przemec Karnowski had 11.
Gonzaga (15-3, 5-1 West Coast Conference) limited Pepperdine to 32 percent shooting.
The Waves (11-8, 4-3 WCC) were led by Stacy Davis with 12 points, the only Pepperdine player in double figures.
Boston schools pull out free condoms over wrapping complaints
NBC reportedly holds celebs hostage to Jimmy Fallon's show