Waters won out at the start, a smart launch from the outside of the front row helping him clear van Gisbergen on the run to Turn 1.
Will Brown actually got the best start of anyone from fourth on the grid and even managed to briefly sneak past van Gisbergen at the first corner.
It was short-lived, though, Brown sliding on the exit of Turn 2, which allowed van Gisbergen to get down the inside into Turn 3.
The top three then ran in formation across the first stint, Waters leading by roughly six-tenths ahead of van Gisbergen and Brown.
On Lap 13 Brown kicked off the stops for the leaders, his hopes of a podium disappearing as he was dropped without his left-rear wheel properly fitted to the car.
That dumped the Erebus driver to the back of the field.
A lap later van Gisbergen made his stop in a bid to undercut Waters, Tickford responding by pitting the Monster Mustang on the very next lap.
The response worked well, Waters popping out just ahead of van Gisbergen before staving off half a lap's worth of intense pressure from the Kiwi.
Waters wasn't able to shake van Gisbergen entirely during the second stint, the Kiwi piling on the pressure in the closing laps.
But track position proved critical as Waters hung on to win ahead of van Gisbergen by just four tenths.
Van Gisbergen, meanwhile, crossed the finish line with a broken front-left wheel thanks to contact with Waters at the last corner.
"It was an awesome race," said Waters. "I got the start and knew I just had to look after the tyres and get it done.
"I knew [van Gisbergen] was probably a little bit quicker so I had to have something in the tank for the end. I knew he would have a crack. It's awesome to come out on top."
Van Gisbergen added: "The battle with Cam was awesome. He's a really good racer, he knows where to place the car. I love that kind of stuff."
David Reynolds made solid gains from seventh on the grid to finish third, just three seconds behind the race winner. That was despite being told to conserve fuel in the closing stages of the race.
The key for the Grove Racing driver was running a long first stint, he and teammate Lee Holdsworth not making their stops until Lap 24 and 25 respectively.
Reynolds then popped out fourth before clearing Chaz Mostert for third.
The best of the wildcards was Jayden Ojeda down in 17th while Jordan Boys was 25th in the other additional entry in the field.
Van Gisbergen leads the Supercars standings by a healthy 196 points over De Pasquale.
The Winton SuperSprint continues with two back-to-back qualifying sessions starting at 9:40am tomorrow.
Winton SuperSprint Race 1 results
|1||6||Cameron Waters||Ford Mustang GT||-|
|2||97||Shane van Gisbergen||Holden Commodore ZB||0.400||0.400||0.400|
|3||26||David Reynolds||Ford Mustang GT||3.032||3.033||2.633|
|4||25||Chaz Mostert||Holden Commodore ZB||11.346||11.347||8.314|
|5||10||Lee Holdsworth||Ford Mustang GT||15.929||15.930||4.583|
|6||20||Scott Pye||Holden Commodore ZB||18.076||18.076||2.147|
|7||99||Brodie Kostecki||Holden Commodore ZB||20.711||20.712||2.635|
|8||11||Anton De Pasquale||Ford Mustang GT||22.791||22.791||2.080|
|9||8||Andre Heimgartner||Holden Commodore ZB||22.942||22.943||0.152|
|10||88||Broc Feeney||Holden Commodore ZB||25.533||25.534||2.591|
|11||17||Will Davison||Ford Mustang GT||25.899||25.899||0.366|
|12||55||Thomas Randle||Ford Mustang GT||33.200||33.201||7.302|
|13||5||James Courtney||Ford Mustang GT||34.175||34.175||0.974|
|14||2||Nick Percat||Holden Commodore ZB||44.929||44.930||10.755|
|15||96||Macauley Jones||Holden Commodore ZB||45.128||45.129||0.199|
|16||3||Tim Slade||Ford Mustang GT||46.528||46.529||1.400|
|17||27||Jayden Ojeda||Holden Commodore ZB||48.579||48.580||2.051|
|18||34||Jack Le Brocq||Holden Commodore ZB||49.316||49.317||0.737|
|19||76||Garry Jacobson||Holden Commodore ZB||51.102||51.102||1.785|
|20||14||Bryce Fullwood||Holden Commodore ZB||51.499||51.499||0.397|
|21||18||Mark Winterbottom||Holden Commodore ZB||52.347||52.348||0.849|
|22||4||Jack Smith||Holden Commodore ZB||55.905||55.906||3.558|
|23||35||Todd Hazelwood||Holden Commodore ZB||56.252||56.252||0.346|
|24||56||Jake Kostecki||Ford Mustang GT||56.653||56.654||0.402|
|25||49||Jordan Boys||Holden Commodore ZB||57.204||57.204||0.551|
|26||22||Chris Pither||Holden Commodore ZB||1'16.936||1'16.936||19.732|
|27||9||Will Brown||Holden Commodore ZB||1'29.877||1'29.877||12.941|
|View full results|