With the game tied at 64, Thompson drilled a 3-pointer with 3:09 remaining to put the Waves ahead for good. Bell and Thompson had seven rebounds each for Pepperdine (5-8).
The Anteaters had taken a 55-50 lead midway through the second half with a 9-0 run highlighted by a steal and layup by Darren Moore, who led UC Irvine (6-5) with 16 points. Patrick Rembert had 10 points and 11 rebounds for the Anteaters.
Lorne Jackson scored 14 points and added nine rebounds for Pepperdine, which led 38-33 at halftime.