A sellout crowd of 4,000 at the Martin Centre watched the matchup between the preseason favorites in the West Coast Conference.
Pepperdine scoring leader Jimmy Miggins, a senior forward coming off a four-point performance -- the lowest of his career -- Thursday night at Portland, led the Waves (9-6, 1-1) with 18 points.
Senior forward Boomer Brazzle added 14 points as the Waves lost to the Bulldogs (11-5, 2-0) for the fifth straight season in Spokane.
Junior guard Blake Stepp, one of five Bulldogs to score in double figures, finished with 16 points and 10 assists.
Junior guard Tony Skinner scored 13 points for Gonzaga, all in the first half, while junior center Richard Fox had 12 points and sophomore forward Ronny Turiaf had 11 points.
Gonzaga never trailed after going on an early 10-point run to take a 14-8 lead. A 20-2 run later in the half gave the Bulldogs a 41-19 lead. They led at halftime, 50-28.
Gonzaga's Tony Skinner scored all 13 of his points in the first half, and Fox, who finished with 12 points, matched his season scoring average of eight points in the opening 5 1/2 minutes.
Gonzaga outshot Pepperdine 55% to 42% and outrebounded the Waves, 42-29, to win for the 46th time in the last 47 home games.