Gonzaga (19-5, 11-2 West Coast) jumped to its largest lead early in the second at 43-30 and led the entire half. Kyle Wiltjer added 17 points and Josh Perkins 10.
Pepperdine (14-10, 7-6) closed within 65-63 on Lamond Murray Jr.'s step-back jumper with 23.6 seconds left in the game.
Kyle Dranginis made a pair of free throws with 18.9 seconds left and Silas Melson's dunk clinched it at 69-63 with six seconds to go. Sabonis made all 12 of his free throws and Gonzaga made 21 of 23.
Stacy Davis led Pepperdine with 26 points and Murray added 15. It was Pepperdine's second straight loss at home after starting the season 9-0.
Gonzaga won for the 31st straight time against Pepperdine going back to 2002.