McLaughlin was held up behind van Gisbergen for the first two thirds of the race. When he finally got by his countryman he got undercut by David Reynolds at the final pit stop. But the Shell V-Power racer put pressure on the Bathurst winner and forced him into a slight error with a little over 20 laps to go to finally grab the race lead.
Reynolds and van Gisbergen tangled late in the race which saw the Kiwi handed a 15 second time penalty for a driving infringement. It capped an awful day for Red Bull Holden Racing, who will finish second in the team's championship to Shell V-Power Racing.
It was the eighth win of the season for McLaughlin and the 16th in his career. He will hold a 78-point lead over Whincup heading into Sunday's final ace.
"A long way to go but yes that was so awesome. I am so pumped," he said.
"Whatever happens tomorrow – we have given it our best shot.
"To get a one-two for Shell V-Power Racing is as good as it gets.
"I really wanted it bad – I got a good start for once in my life and we were going alright but then pit lane – it was a bit tight in places but to get the first race is awesome."
Reynolds was left fuming with van Gisbergen. The pair have a long history of ill-feeling and he didn't hold back in post-race interviews.
"Pretty disappointed because if we got another podium the team bonus would have been $30-50K so that cost us a lot of money," he said.
"I am very pissed off – very ordinary driving from old mate – we wouldn't expect anything less from that dude to be honest."
Sunday features qualifying, a top 10 shootout and a 95-lap race to conclude the season.