Waters was the big winner at the start, bolting into the lead through Turns 1 and 2 as he left van Gisbergen scrapping over second with Andre Heimgartner.
It was a scrap that Heimgartner was up for, too, demoting his fellow Kiwi to third on the exit of Turn 2 before covering smartly into Turn 3 to seal second place.
Heimgartner was initially able to match Waters for pace, the pair separated by around eight tenths for the first five laps.
However around that point Waters was able to break clear, his lead growing as Heimgartner dropped back to van Gisbergen.
On Lap 14 the two New Zealanders traded places, van Gisbergen sliding under Heimgartner on the exit of the sweeper to reclaim second place.
At that point the lead was just under three seconds, but van Gisbergen quickly made inroads on Waters.
The lead was down to around 1.5s on Lap 18 when Waters elected to take his mandatory stop.
For the first time this weekend van Gisbergen went for an overcut, staying out for an extra four laps before hitting the lane.
But his stop itself was costly, a decision to take on three tyres allowing Heimgartner, who stopped on the same lap, to get out ahead.
It didn't take long for van Gisbergen to clear Heimgartner, but it did mean he was well over five seconds adrift of Waters as the stops shook out.
The additional grip from the three-tyre strategy meant van Gisbergen could consistently reel Waters in during the second stint.
But he couldn't quite run the Monster Mustang down, Waters holding on to win by just four-tenths in a finish that was similar to yesterday's opener.
"I'm so pumped to get it done again," said Waters. "Two wins this weekend, absolutely amazing.
"I know Shane took three tyres, I knew he was going to come back at me. He was fast in that first stint. I just tried to press on, maintain as much of a gap as I could, and I held on."
Heimgartner came home a somewhat lonely third while David Reynolds was similarly lonely in fourth place.
Erebus pair Brodie Kostecki and Will Brown were next on the road, however Kostecki was dumped down to 13th, and Brown promoted to fifth, in the final results due to a time penalty for speeding in pitlane.
Van Gisbergen now leads De Pasquale in the standings by 281 points, while Waters is now third, another 52 points back.
The season continues next month with the Darwin Triple Crown.
Winton SuperSprint Race 3 results
|1||6||Cameron Waters||Ford Mustang GT||-|
|2||97||Shane van Gisbergen||Holden Commodore ZB||0.442||0.442||0.442|
|3||8||Andre Heimgartner||Holden Commodore ZB||10.732||10.733||10.290|
|4||26||David Reynolds||Ford Mustang GT||15.256||15.256||4.524|
|5||9||Will Brown||Holden Commodore ZB||25.565||25.565||10.309|
|6||10||Lee Holdsworth||Ford Mustang GT||27.756||27.757||2.191|
|7||88||Broc Feeney||Holden Commodore ZB||28.705||28.706||0.949|
|8||11||Anton De Pasquale||Ford Mustang GT||29.024||29.024||0.318|
|9||18||Mark Winterbottom||Holden Commodore ZB||34.190||34.190||5.166|
|10||17||Will Davison||Ford Mustang GT||35.437||35.437||1.247|
|11||25||Chaz Mostert||Holden Commodore ZB||36.616||36.616||1.179|
|12||55||Thomas Randle||Ford Mustang GT||39.024||39.025||2.409|
|13||99||Brodie Kostecki||Holden Commodore ZB||39.276||39.276||0.251|
|14||20||Scott Pye||Holden Commodore ZB||41.858||41.858||2.582|
|15||2||Nick Percat||Holden Commodore ZB||43.610||43.610||1.752|
|16||76||Garry Jacobson||Holden Commodore ZB||45.407||45.407||1.797|
|17||34||Jack Le Brocq||Holden Commodore ZB||45.642||45.642||0.235|
|18||35||Todd Hazelwood||Holden Commodore ZB||50.638||50.638||4.996|
|19||96||Macauley Jones||Holden Commodore ZB||53.833||53.833||3.195|
|20||3||Tim Slade||Ford Mustang GT||58.791||58.791||4.958|
|21||27||Jayden Ojeda||Holden Commodore ZB||59.177||59.177||0.386|
|22||22||Chris Pither||Holden Commodore ZB||59.506||59.506||0.329|
|23||14||Bryce Fullwood||Holden Commodore ZB||59.524||59.525||0.019|
|24||49||Jordan Boys||Holden Commodore ZB||1'02.336||1'02.337||2.812|
|25||56||Jake Kostecki||Ford Mustang GT||1'02.636||1'02.636||0.300|
|26||4||Jack Smith||Holden Commodore ZB||1 lap|
|27||5||James Courtney||Ford Mustang GT||5 laps|
|View full results|