Utah Valley (4-5) got five 3-pointers from Hunsaker, one in overtime, and 19 points and nine rebounds from Ben Aird.
Aird sent the game into the extra session with a pair of free throws with 39 seconds left in regulation to tie the score at 55.
Pepperdine (4-3) had a four-game winning streak snapped.
Lorne Jackson led Pepperdine with 17 points, allowing him to become the 37th player in school history to reach the 1,000-point at level.
Stacy Davis had his second straight double-double with 12 points and 12 rebounds, and Caleb Willis had 12 points and nine rebounds.