Lamond Murray Jr. added 17 points and Jett Raines scored 12 for Pepperdine.
Marcus Harris hit a 3-pointer to give San Diego (6-14, 1-8 West Coast Conference) a 5-2 lead, but the Waves scored the next nine points, and later used a 14-5 run to push their lead to 17, 42-25, with 2:33 left in the half.
Jito Kok hit a jumper that pulled the Toreros within seven with 13:56 to play before Pepperdine (14-7, 7-3) used a 13-2 run over the next six-plus minutes to make it 67-49.
Olin Carter III scored 15, Alex Floresca added 13 on 5-of-5 shooting, Kok had 12 points and Harris 10 for San Diego.
Davis finished with six rebounds and moved into fifth on school's career list with 877.