Cavic had three steals, sank four 3-pointers and went seven of 10 from the field. San Franciscos Alan Wiggins Jr. tallied nine rebounds.
Late in the game, the Waves had a chance to tie at 70 but turned the ball over with 29 seconds left.
Surratt then sank two free throws to put the game away for the Dons (7-11, 3-0), who have opened conference play with three wins for the first time since 1991.
After the Dons built a 38-36 halftime lead, Pepperdine took an eight-point lead early in the second half. But San Francisco surged back on an 11-0 run.
San Francisco had 12 steals to Pepperdine's five.