Kevin Bailey scored 15 points, Thomas van der Mars had 12, and Volodymyr Gerun and Bryce Pressley chipped in 10 apiece for Portland (15-10, 6-7 West Coast Conference), which shot 51 percent from the floor.
A 10-2 surge gave Portland a 52-40 lead midway through the second half. Amadi Udenyi scored eight straight points to pull Pepperdine within 54-48 with 7:59 left. But the Waves went cold from there, missing 12 of their last 14 shots.
Stacy Davis scored 18 points on 8-of-11 shooting, and grabbed 10 rebounds to lead Pepperdine (15-10, 8-6 West Coast Conference). Udenyi had 14 points and Jeremy Major added nine points with five assists and three steals for the Waves.