The one-two finish for the Ford Performance Racing team - their first at an endurance event - means the title seems destined for their garages.
Winterbottom moves 198 points ahead of Mostert, with Craig Lowndes slipping to fourth after David Reynolds jumped into third overall in the championship after finishing fifth with co-driver Dean Canto.
Lowndes and co-driver Steve Richards couldn't move far from their poor qualifying effort, finishing 13th.
Reynolds is 360 points behind series leader Winterbottom, while reigning champion Whincup slumps to eighth and 629 points off the pace.
Mostert's second place owes much to co-driver Waters, 21.
The car's fuel strategy shuffled the youngster back through the field but he steadily moved back up the order, improving five positions in 10 laps.
After the co-drivers made way for the championship hunters, a key moment arrived on 86 laps when Alex Buncombe put his Nissan in the tyre wall and brought the day's first safety car. The gap between the top four fell from 20s to less than two at the restart, aiding the Ford assault.
The biggest drama of the day spoiled Scott McLaughlin's race.
Co-driver Alex Premat pitted for fuel but a refuelling bungle saw one of his crew leave the spike in the Frenchman's Volvo, requiring him to pit again to get it removed and serve another pit-lane penalty.