Marc Trasolini scored 21 points and Evan Roquemore made four free throws in the final 40 seconds to help Santa Clara hold off Pepperdine 71-68 on Saturday night.
Kevin Foster added 16 points and five assists despite an off night shooting as the Broncos completed their first sweep of the Waves since 1984.
Santa Clara (18-13, 8-6 West Coast Conference) locked up the No. 4 seed and a first-round bye in the league tournament beginning next week in Las Vegas.
Lorne Jackson had 23 points for Pepperdine (11-20, 5-9), which lost its fourth straight.