Olynyk scored 14 points in the second half as the Bulldogs (14-1, 1-0 WCC) won despite shooting a season-low 43.4 percent from the field. Reserve guard David Stockton added nine points and four steals and Kevin Pangos scored nine points.
Pangos gave Gonzaga the lead for good at 38-36 on a 3-pointer and the Bulldogs pulled away to their 23rd consecutive win against Pepperdine, its longest streak against a conference opponent.
Lorne Jackson led the Waves (8-6, 0-1) with 16 points and Jordan Baker had 15.
Jackson kept the Waves in it for much of the second half. He made consecutive baskets on a 3-pointer and a long jumper from the corner to get the Waves within 43-41. Another long jumper from Jackson made it 50-45.
Gonzaga appeared to grab momentum when Pepperdine turned it over out of a timeout with 8:22 to go. Mike Hart missed inside, sprawled to collect his own rebound and passed it out to Pangos for a 3-pointer and a 57-47 lead.
Gonzaga made 25 of 29 free throw attempts and shot 56 percent from the field in the second half.
Gonzaga managed through a poor-shooting first half and took a 30-26 lead into halftime. The Bulldogs, ranked second nationally in field goal percentage, shot 37.1 percent and was 3 for 11 from 3-point range.
Stockton put them in the lead at 23-21 with a driving layup and a runner off a Pepperdine turnover. He had three steals as Gonzaga forced Pepperdine into 11 first-half turnovers.
Gonzaga missed 11 of its first 14 shots and fell into a 14-6 deficit. Przemek Karnowski helped get it going with a left-handed hook shot and a basket inside before Stockton made a 3-pointer. Hart's 3 gave Gonzaga its first lead at 19-18.
Pepperdine sat Jackson, its leading scorer. to start the game and started 7-foot center Jan Maehlen for the first time this season in order to try and counter Gonzaga's size.