Thompson had 23 points and 10 rebounds while Jackson finished with career highs of 23 points and 10 assists for the Waves (6-11), who ended a three-game losing streak.
Leading 68-61 with 4½ minutes to go, Pepperdine put the game away with a 10-0 run.
The Waves never trailed in the first half and went up by as many as 12 before taking a 41-40 lead at the break. Seattle took its only lead, 45-43, on a 3 by Carter early in the second half. A layup by Jackson with 18:22 left put Pepperdine up 47-45, and the Waves led the rest of the way.