The Bulldogs (6-6, 5-3) built an early lead as Waller and Josh Quezada each ran for scores and Brian Burrell threw a 6-yard touchdown pass to Justin Johnson in between. Waller's second touchdown capped a 15-play, 96-yard drive to take a 28-0 halftime lead.
Hawaii (4-9, 3-5) stormed back in the fourth quarter as Ikaika Woolsey threw three touchdown passes. His 2-yard scoring pass to Quinton Pedroza pulled the Warriors within seven with 45 seconds left. Fresno State recovered the ensuing onside kick to hang on.
Josh Harper had 83 yards on eight receptions for Fresno State.
Woolsey threw for 247 yards with two interceptions, including one in the end zone on Hawaii's opening drive of the third quarter.