Jett Raines contributed 13 points and Atif Russell added 10 for Pepperdine (12-6, 5-2 West Coast Conference). The Waves shot just 39 percent on 51 attempts from the field, lost the rebound battle 36-32 but edged Portland 22-13 in made free throws.
Portland (11-8, 2-5) shot 42 percent from the floor and hung on to a narrow lead much of the second half.
But late in the period, Pepperdine closed a six-point deficit and tied it at 52 on a dunk from Raines, who followed it up with the go-ahead 3-pointer with 3:33 to go. The Waves protected the advantage down the stretch with 12-of-16 shooting from the free throw line.