The Toreros (8-12, 3-5 WCC) began to pull away midway through the first half and extended its lead to 37-21 at halftime. San Diego shot 56.0 percent in the first half while holding the Waves to 34.6 percent shooting.
Taylor Darby scored 13 of his 15 points in the second half to lead Pepperdine (7-13, 1-8), whose losing streak reached eight games. During the streak, the Waves have lost by average of 16 points per game.
Johnny Dee added 12 points for San Diego, which snapped a four-game home losing streak and won for just the third time in 11 games.
Pepperdine, whose last win was in the conference opener against San Francisco on Dec. 29, cut the lead to 42-35 early in the second half but never got closer.