Waters led the early stanza of the race, only to be overtaken at Turn 6 by the championship leader.
The Tickford Racing driver battled to sixth, with Jamie Whincup making it a Red Bull Ampol Racing one-two.
The early laps suggested van Gisbergen’s winning run would be halted, with Waters forcing his way into an early lead.
WATCH: BOTTLENECK INTO TURN 2
Whincup demoted van Gisbergen to third, only for the #97 Red Bull Ampol entry to assume second in quick time.
Waters led, but van Gisbergen kept a watching brief in second before pouncing for the lead at the end of lap 9.
The Monster Energy Mustang fell into the clutches of Whincup, who made a bold move at Turn 6.
Waters wins the start
Chaz Mostert, who started third, followed Whincup through, albeit with a locked front tyre.
At the end of lap 17, Whincup was the first of the leading group to pit.
Waters stopped on lap 21, and was undercut by both Shell V-Power Racing Team Mustangs, with Anton De Pasquale firming for a first podium for his new team.
WATCH: WATERS LOSES TWO SPOTS IN ONE GO
Mostert was also undercut by the Shell Fords after his lap 22 stop, but managed to leapfrog Waters.
Van Gisbergen pitted on lap 23, and having managed his tyres to perfection, emerged ahead of Whincup to retain the Red Bull Ampol one-two.
The formation remained until the chequered flag, van Gisbergen cruising to victory in the 44-lap sprint by over four seconds.
WATCH: DICEY DJR REJOIN
De Pasquale defied Mostert to clinch his maiden Dick Johnson Racing podium, with Will Davison holding onto fifth ahead of Waters.
Mark Winterbottom and Scott Pye made it a Team 18 seven-eight, with Erebus Motorsport duo Will Brown and Brodie Kostecki completing the top 10.