Talking point of the weekend was Erebus driver Lee Holdsworth's big shunt towards the end of the race. Holdsworth got out of shape at over 260km/h and smacked heavily into the barrier, destroying the car.
Luckily for Whincup, three lapped cars stood between him and Courtney at the restart, giving him an advantage over the HRT driver.
"The lapped traffic wasn't that keen on getting out of the way," said Courtney. "I think they wanted to un-lap themselves. It hindered us a little for the run at the end there, but that's the way it is."
Whincup has now won seven of the last 13 races since he took the championship lead from Winterbottom and now has a comfortable 273-point buffer over Lowndes.
The series now heads for the second leg of the Pirtek Enduro Cup - the Bathurst 1000 - from October 9 to 12.