The Triple Eight driver set the foundation for the unlikely win with a fast start from the sixth row, capped off with a brave move on Scott McLaughlin for seventh place at the end of the first lap.
While McLaughlin bailed out of the battle early, pitting on Lap 7 for clear air, van Gisbergen went the other way. He didn't stop until Lap 24, giving him poor track position, but great tyre condition, for the run home.
Initially it looked as if McLaughlin's strategy was the winner, the Penske Ford driving undercutting everyone to come out in front.
But a late Safety Car to retrieve Anton De Pasquale's car from the Turn 6 barrier proved to be his undoing, bringing the likes of pole-sitter Todd Hazelwood, Jamie Whincup and van Gisbergen – who was ninth at the restart – back into the game.
When the race went green again nine laps from home McLaughlin still looked like he might have enough in the tank, particularly after holding off a brief challenge from Hazelwood.
But once the two Triple Eight cars cleared the Brad Jones Racing entry their pace was unleashed, Whincup letting van Gisbergen through four laps from home to have a crack at the leader.
It proved to be a shroud move, van Gisbergen not only using his superior grip to pass McLaughlin at Turn 12 on the same lap, but running the Mustang wide so that Whincup could sneak into second.
With no team orders in play van Gisbergen was free to storm to victory, winning from further back on the grid than anybody's ever managed in Townsville.
"What an awesome race," said van Gisbergen, who hadn't won a race all season before today's opener.
"I had a great car. I got stuck in the first stint, but the Safety Car worked out perfectly. It was a big battle at the end trying to do the team thing to help Jamie."
McLaughlin clung on to third despite a late challenge from Chaz Mostert, but was left unimpressed with van Gisbergen's move.
"Shane was playing the team game there," he said. "He's made plenty of clean passes there over the years, and that was pretty average. Just a big push off at the end there.
"I get that he's playing the team game, but it would have been nice a bit more of a fair battle."
McLaughlin still leads the series by 143 points over Whincup with just three events to go.
Scott Pye was a big mover once again, turning 17th on the grid into fifth, while Hazelwood went the other way, dropping back to sixth as the finish.
Nick Percat, who started alongside his teammate on the front row, came home seventh ahead of Fabian Coulthard, James Courtney and Lee Holdsworth.
|1||97||Shane van Gisbergen||Holden Commodore ZB|
|2||88||Jamie Whincup||Holden Commodore ZB||0.994|
|3||17||Scott McLaughlin||Ford Mustang GT||3.032|
|4||25||Chaz Mostert||Holden Commodore ZB||3.454|
|5||20||Scott Pye||Holden Commodore ZB||6.837|
|6||14||Todd Hazelwood||Holden Commodore ZB||7.660|
|7||8||Nick Percat||Holden Commodore ZB||8.100|
|8||12||Fabian Coulthard||Ford Mustang GT||9.451|
|9||44||James Courtney||Ford Mustang GT||10.015|
|10||5||Lee Holdsworth||Ford Mustang GT||12.073|
|11||9||David Reynolds||Holden Commodore ZB||12.078|
|12||6||Cameron Waters||Ford Mustang GT||13.085|
|13||18||Mark Winterbottom||Holden Commodore ZB||14.138|
|14||55||Jack Le Brocq||Ford Mustang GT||14.712|
|15||19||Alex Davison||Holden Commodore ZB||15.074|
|16||15||Rick Kelly||Ford Mustang GT||15.616|
|17||7||Andre Heimgartner||Ford Mustang GT||16.084|
|18||2||Bryce Fullwood||Holden Commodore ZB||17.151|
|19||3||Macauley Jones||Holden Commodore ZB||18.346|
|20||35||Garry Jacobson||Holden Commodore ZB||19.361|
|21||4||Jack Smith||Holden Commodore ZB||19.766|
|22||34||Jake Kostecki||Holden Commodore ZB||20.366|
|99||Anton De Pasquale||Holden Commodore ZB|
|22||Chris Pither||Holden Commodore ZB|
|View full results|