Whincup crashed out in tricky conditions before heavy rain arrived, while Nick Percat's Holden caught fire in pitlane in the closing stages.
A second victory for Holden this year also ends McLaughlin's winning streak of six races.
"It's been a tough year for us. We're getting better, but that one wasn't me for sure, it was Shippy (engineer Grant McPherson) and the boys," van Gisbergen said.
"I was really struggling, struggling to keep my head when we didn't have the grip. They kept it under control and kept me focused until the end. That's a real team victory."
Light rain fell as the race started, but it was not heavy enough to sway drivers from setting off on slick tyres.
That was soon the least of McLaughlin and Reynolds' worries, the pair tangling into Turn 2 on the opening lap as the latter looked down the inside.
McLaughlin limped back to pitlane with a puncture but remained on the lead lap, while Reynolds lost four laps repairing a broken steering arm.
Stewards took no action on the incident.
Polesitter Waters bolted at the front, leading by four seconds after the first two laps.
His lead over Coulthard then stabilised, while Mostert was the big mover into third from 16th, including moving up to sixth on lap one.
Coulthard clawed Waters' advantage back as the track dried out to be right behind the Monster Mustang when they pitted together on lap 18.
The Shell Ford emerged ahead, just before Whincup crashed at Turn 6 and then stopped on track, bringing out the Safety Car.
Amid the subsequent pitstops, McLaughlin went a lap down based on taking on a significant fuel load.
Rain intensified after the restart, and Waters reclaimed the lead on lap 30 amid a mass of pitstops for wet tyres.
De Pasquale had stopped for that tyre change during the Safety Car period and duly vaulted into the lead, with a 35s buffer back to Waters at the halfway mark.
While De Pasquale circulated at the front, still needing more fuel, van Gisbergen capitalised on a Waters error to take second, ahead of Coulthard, Mostert and Waters.
De Pasquale had a pair of offs during the middle phase of the race, as van Gisbergen, Coulthard and Mostert ate into his lead.
Mostert picked his way past Coulthard and van Gisbergen to run second to De Pasquale, before pitting on lap 60 to complete his minimum fuel drop.
Garry Jacobson's Nissan stopped at the same time to prompt another Safety Car period, as De Pasquale came in to make his extra stop.
The race did not restart, van Gisbergen picking up first place and leading Coulthard across the line to secure his 33rd career victory.
Van Gisbergen moves back into third in the championship with the victory.
Coulthard remains second, 292 points behind McLaughlin, after taking second in his 400th Supercars race.
"You had to be on the right tyres at the right time," Coulthard said.
"The boys asked me if I wanted to pit for wets and I was like 'no, yes, yes, no', and finally said 'yes, let's just commit' and it turned out to be the right call."
Waters grabbed a fifth podium of the season, edging past De Pasquale as the latter's Penrite Holden left pitlane.
Mostert wound up fifth, ahead of the lead Nissan of Rick Kelly.
Boost Mobile Racing pair James Golding and Michael Caruso finished seventh and ninth, split by Lee Holdsworth, who lost time with a later stop for wet tyres.
Simona De Silvestro rounded out the top 10, despite being turned around by Tim Slade in the final stint.
A time penalty for Slade elevated McLaughlin from 12th to 11th, the championship leader banking valuable points after getting back on the lead lap.
There was late drama when Percat's car caught fire during a late extra stop after a fuel rig issue.
The Brad Jones Racing Commodore stopped at the end of pitlane while rival crews helped extinguish the flames.
