Coulthard made up a number of spots to salvage a reasonable result. He finished ninth having started the race outside the top 20.
Both Shell V-Power Fords struggled in the wet on Saturday and in qualifying on Sunday but they had better race pace.
McLaughlin ran out of fuel on his celebration lap to further prove just how perfectly his team had judged the fuel situation.
He was grateful to co-driver Premat for his impressive early stint and the result goes a small way to making up for the heart-breaking engine failure at Bathurst a fortnight ago.
"Alex Premat did an unbelievable job in the first stint and that set us up," a delighted McLaughlin said. "Thanks to everyone at Shell V-Power Racing - oh my god this is so good after Bathurst.
"I just wanted to maintain the gap and I managed to hold on at the end there," he added in relation to the fuel situation.
Whincup conceded that his rivals played the better game today but will be extremely happy to leave the Gold Coast with the championship lead.
"We are happy with the result but pace and being a bit more aggressive on strategy - yeah they deserved the win - congrats to them," Whincup said.
Supercheap Ford driver and Saturday race winners Chaz Mostert and Steve Owen claimed the Pirtek Endurance Cup as a result of their all-round performances across the Sandown 500, Bathurst 1000 and Gold Coast 600 events.
The series moves to New Zealand for the penultimate round of the series at Pukekohe Park Raceway in a fortnight with the title fight wide open. Just 27 points separates the top three drivers while even Mostert and van Gisbergen are not out of the equation with 600 points still up for grabs.
Championship Standings
Jamie Whincup 2580
Fabian Coulthard -17
Scott McLaughlin -27
Chaz Mostert -126
Shane van Gisbergen -189