Corbin Moore posted 11 points and nine rebounds as Pepperdine handed Northern Arizona a 49-40 defeat on Wednesday night.
Moore added three blocks as the Waves (5-3) took advantage of the undersized Lumberjacks (2-7) in the paint.
Pepperdine, which leads the all-time series 13-3, held a 38-28 rebounding advantage and tallied seven blocks.
James Douglas and Stallon Saldivar scored 10 points each for Northern Arizona.
The Lumberjacks lost their fourth straight and remained winless against Division I opponents, shooting a season-low 28.8 percent from the floor and 13.3 percent from 3-point range.
The Waves led 25-15 at halftime as the Lumberjacks were just four points shy of their lowest-scoring half ever. They posted 11 points in both halves of a 28-22 loss to Weber State in 1980.
Northern Arizona pulled within three, 31-28, on Douglas' 3-pointer from the wing with 14:36 left, but Pepperdine quickly regained momentum on Nikolas Skouen's driving layup and deep 3-pointer.
Skouen was the Waves' second-leading scorer with eight points.
The Lumberjacks nudged within four points twice in the final five minutes. But Hector Harold helped silence the threats with a putback and a 3-pointer from the corner, with the latter sparking an 8-0 run.
