The Bulldogs (14-1) opened West Coast Conference play by defeating the Waves for the 23rd straight time.
Gonzaga had only a one-point lead with 11:45 to play, but finished the game with a 35-20 run.
Harris made all six of his foul shots and scored 18 points. Kelly Olynyk added 16 for the Bulldogs, whose lone loss this season came on Dec. 8 against Illinois.
Pepperdine (8-6) put together its best non-conference record in eight seasons, but hit only 2-of-12 from 3-point range.
Lorne Jackson led Pepperdine with 16 points and Jordan Baker had 15.