The subsequent repairs and a pitlane penalty left Winterbottom visibly upset as he was left to circulate several laps down for the majority of the 102-lap event.
The result means Winterbottom's 399-point lead heading into the race has been whittled down to 306 points in a single day.
Up front, the Tekno Autosports entry of Van Gisbergen and Jonathon Webb was unstoppable.
The pair, who won on the streets of Surfers Paradise last year, were never challenged as they finished a second and a half ahead of Reynolds.
"It wasn't just me," said van Gisbergen, who won by 1.6 seconds. "We came in with a 10-second lead, the car was amazing. To do those times lap after lap, the car was just fantastic."
Of the other Kiwis, Fabian Coulthard and Luke Youlden finished seventh and Scott McLaughlin and Alexandre Premat a disappointing 21st after McLaughlin, who started in second on the grind after an excellent qualifying lap, was once again beset by car troubles.
Lowndes came in third after threatening to overtake Reynolds in the race's closing stages with Tander hot on their heels in fourth.
Defending champion Jamie Whincup could only limp home in 24th position after his co-driver Paul Dumbrell was involved in an early incident.
He had arrived at the Gold Coast 600 hoping to erase memories of a Bathurst nightmare earlier in October, when he was running second in the 1000km classic when he disobeyed a team order to pit and then copped a penalty for passing the safety car. He would finish 18th.
Things began well yesterday, with Whincup qualifying second-fastest for the top 10 shootout for pole position at the Gold Coast.
He then produced one of the ugliest single laps of his recent V8s career in the shootout to settle for seventh position on the grid.
Handing over to co-driver Paul Dumbrell for the race start, Whincup could only watch from the garage as a collision between his Commodore and Ford driver Dean Canto cruelled their hopes.
Dumbrell limped back to the pits but a lengthy repair left Whincup to circulate several laps behind the rest of the field for the remainder of the 102-lap race.
"Can't get a break. It's just been one of those years unfortunately," Whincup said.
The Gold Coast 600 wraps up today with a second 300km race.
- AAP