A downpour shortly before the start of the finale meant the race initially got underway behind the safety car. That only last two laps, though, the race going green with Waters in the lead on lap three.
The second half of the opening lap saw three different leaders in what was a brilliant scrap between Waters, van Gisbergen and Anton De Pasquale.
First it was De Pasquale that lunged Waters to lead, only for the Shell Ford driver to then drop back to fourth was Waters, van Gisbergen and Feeney got through.
Van Gisbergen then briefly led over Waters before the Tickford driver got back through on the main straight.
Waters and van Gisbergen continued to battle for the next two laps until van Gisbergen ran slightly wide on lap five and Feeney snuck into second.
The rookie then slid off the road on the next lap, allowing van Gisbergen to pick up the battle for the lead with Waters.
Van Gisbergen briefly got ahead again on lap seven and then at the start of the next lap, but couldn't make either move stick.
The Kiwi kept the pressure on for the next three laps until Waters finally ran too deep into the penultimate corner.
He kept his car on the road but the slight delay was enough for van Gisbergen to sneak through into the lead.
Once in front there was no stopping van Gisbergen, his lead over two seconds within a couple of laps before ballooning from there.
He took his stop on lap 23, the penultimate lap, before cruising to a 8.7s victory.
"That was awesome," said van Gisbergen of the early battle with Waters. "It's always good racing someone who has nothing to lose. He drives hard, but respectful as well.
"It was awesome. Once I got in front I struggled a bit with no train tracks to follow, but then I pulled away.
"What an awesome weekend, I can't thank the team enough. I've struggled with feeling in the car all weekend but it's been super fast."
Waters cruised to second place ahead of Erebus driver Brodie Kostecki, who was impressive in tough conditions on his way to third.
Will Davison and Chaz Mostert both put in stirring drivers after an early coming together. Mostert got into the back of Davison during the frantic early laps, the Shell Ford left facing the wrong way as Mostert copped a 15-second penalty for his efforts.
Davison spun again while beginning his recovery but was then able to charge through to finish fourth, ahead of Feeney and Will Brown.
Mostert, meanwhile, charged through the field after serving his penalty to finish a remarkable eighth, right behind De Pasquale. Nick Percat and Lee Holdsworth rounded out the top 10.
James Golding and David Reynolds looked to be on for good results midway through the race as they charged into the top 10.
However they had a coming at Turn 6 in the second half of the race which dropped Golding back to 14th, and forced Reynolds into the pits with significant damage. He was ultimately classified 22nd, four laps down.
There was trouble between the Matt Stone Racing team-mates, meanwhile, with Todd Hazelwood taking Jack Le Brocq out of the race in the early stages. Hazelwood kept going but could only manage 21st.
Wildcard Zak Best was classified last after being withdrawn from the race due to a broken wiper motor.
Thanks to his latest victory van Gisbergen will take a 393-point lead over Waters to the next round of the series at Sandown Motor Raceway on 19-21 August.
Shane van Gisbergen, Triple Eight Race Engineering
Photo by: Mark Horsburgh, Edge Photographics
Van Gisbergen wins crash-shortened Race 2
Shane van Gisbergen won a second Supercars race at The Bend that was marred by a nasty start line crash.
The race got off to a dramatic start when front-row starter Thomas Randle stalled on the line.
As the field scrambled to get past the stricken Castrol Ford, Andre Heimgartner was caught by surprise, smacking square into Randle's right-rear.
The high-speed impact not only destroyed both Randle and Heimgartner's cars, but also meant Randle clipped Nick Percat as he tried to sneak by on the outside.
Thankfully all three drivers emerged from their wrecked cars without any serious injuries.
The race was red-flagged while the crashed cars were cleared, before a full standing restart.
The winner from the restart was Mostert, who fired from the outside of the third row to the lead with a bold move up the inside of Turn 1.
James Courtney made a smart start as well to move into second, while polesitter Cam Waters was shuffled back to fifth, behind Anton De Pasquale and Shane van Gisbergen, on the opening lap.
Courtney and De Pasquale were the first of the lead group to pit, each taking their mandatory service on lap 5.
Mostert then surrendered the lead to cover those cars by stopping a lap later, resuming ahead of both Courtney and De Pasquale.
Waters waited until lap 11 to make his stop, popping back out between Courtney and De Pasquale in what was effectively fourth place.
Like race one van Gisbergen ran long, not taking his stop until lap 16.
He was able to resume comfortably clear of Mostert and Courtney, before cruising through the next two laps to take a time certain chequered flag.
Mostert and Courtney were second and third ahead of Waters and De Pasquale.
Broc Feeney finished sixth while Will Brown was the best of the Erebus cars in seventh. David Reynolds finished eighth, Mark Winterbottom ninth and Bryce Fullwood 10th.
Jordan Boys was the best of the wildcards in a credible 11th while Will Davison recovered from 23rd on the grid, and a spin on the restart lap, to finish 13th.
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