Coltrane Powdrill led the Kingsmen with 22 points and Arik Smith added 10.
Murray scored 12 points in the first half, including three buckets in a row, and Pepperdine used a 9-2 run to pull to a 36-26 halftime lead.
The Kingsmen pulled to within four points three times in the second half before Shawn Olden hit a pair of free throws at 10:20 and Murray made a jumper as part of an 8-2 run for a 57-48 Pepperdine lead. The Waves finished with a 10-2 run that included a dunk by Raines.
Pepperdine outshot Cal Lutheran to 37.1 percent to 35.5 percent from the field.