With the Safety Car taking control of the race, the majority of the field dived into the lane.
Van Gisbergen, Slade and Davison emerged ahead of Waters, who dropped to effective fourth following a long stop.
Waters took on 77 litres, but his team raised the bonnet, enabling the longer fuel stop. Whincup was forced to double stack, took on 83 litres and was buried in the midfield by the lap 10 restart.
Waters returned to lane during the full course yellow, with Tickford initially diagnosing a power steering issue.
He returned to the race, albeit five laps down, on lap 15. All the while, van Gisbergen stretched his legs in the lead, with Bryce Fullwood, who only took on 21 litres, rising to second after starting 12th.
Several drivers took advantage of the Safety Car period, with Le Brocq up nine spots into sixth, Reynolds up six spots in seventh, and Zane Goddard, who stopped on lap 6, up nine places.
Smarting after being forced to double stack, Whincup pressured Fabian Coulthard, who had jumped from 20th to 12th amid the pit stops.
Whincup made the move at the final corner at the end of lap 17, and was released into clear air.
At the end of lap 19, Walkinshaw Andretti United pulled Fullwood in from second, triggering the second round of stops.
Reynolds stopped one lap later from sixth, with Le Brocq, Hazelwood, Goddard and Heimgartner all stopped on the following lap.
The latter was slapped with a drive-through penalty for a dangerous release, with the #7 NED Whisky Mustang pulling outing front of Brodie Kostecki following an off at the first corner.
The front-runners began to blink; Davison pitted from third at the end of lap 26, two laps after Slade made his final stop.
On lap 28, van Gisbergen was brought in for his defining second stop, and emerged 11 seconds ahead of Davison, with Slade shadowing the #17 Shell V-Power Racing entry.
Mostert peeled in from the lead on lap 30, and filtered out with a six-second margin over Davison.