Kai Healey and KJ Feagin scored 11 apiece for Santa Clara (6-12, 2-4 West Coast Conference). Healy made a career-high three 3-pointers.
Healey and Matt Hauser scored five points each during a 14-2 run that gave the Broncos a 50-36 lead with nine minutes to play.
A 3-point play by Brett Bailey pulled the Toreros within eight with 50 seconds left, but Kratch and Feagin combined to make 4 of 4 free throws from there to seal it.
Bailey led San Diego (5-10, 0-4) with a career-high 22 points, on 9-of-16 shooting, and eight rebounds.
Santa Clara made 23 of 45 (51 percent) field goal attempts while limiting San Diego to 38 percent (21-of-56) shooting.