In the first of two 10-minute sessions the two Red Bull Holden stars locked out the front row, van Gisbergen's 1m55.224s leading Whincup by 0.08s.
The seven-time champion was lucky to get that far, a brush with the wall on the exit of Turn 10 leaving his Commodore with a bent rim.
It did nothing to dent Whincup's confidence, though, a 1m55.280s in the second qualifying session handing him pole for the Saturday morning race.
Van Gisbergen slipped back to fourth in the second session, beaten by Tickford pair Cam Waters and Will Davison.
"Obviously both cars are really strong," said Whincup. "Full credit to the engineers, they brought us some rockets.
"I didn't quite have a good rhythm in the first one and belted the wall as a result. Once we changed the tyre set the car was back to brand new [for the second session], and really good through the middle sector."
Scott McLaughlin was consistent across the two sessions with a fourth and a fifth, while Andre Heimgartner banked a pair of Top 10s with a fifth for Race 1 and ninth for Race 2.
Chaz Mostert did likewise, qualifying 10th for the first race before staging his own shootout-style lap, after everyone had set a time, to take seventh in the second.
David Reynolds was the least consistent of the front-runners, the Erebus driver losing his crucial lap in the first session with a track limits infringement.
His second lap on the tyre set was only good enough for 17th, before he grabbed sixth on the grid for the second race.
First qualifying results:
|1||97|| Shane van Gisbergen ||Holden Commodore ZB||1'55.224|
|2||88|| Jamie Whincup ||Holden Commodore ZB||1'55.313||0.089|
|3||23|| Will Davison ||Ford Mustang GT||1'55.318||0.094|
|4||17|| Scott McLaughlin ||Ford Mustang GT||1'55.436||0.212|
|5||7|| Andre Heimgartner ||Ford Mustang GT||1'55.533||0.309|
|6||99|| Anton De Pasquale ||Holden Commodore ZB||1'55.572||0.348|
|7||8|| Nick Percat ||Holden Commodore ZB||1'55.689||0.465|
|8||6|| Cameron Waters ||Ford Mustang GT||1'55.781||0.557|
|9||5|| Lee Holdsworth ||Ford Mustang GT||1'55.784||0.560|
|10||25|| Chaz Mostert ||Holden Commodore ZB||1'55.822||0.598|
|View full results|
Second qualifying results:
|1||88|| Jamie Whincup ||1'55.280|
|2||6|| Cameron Waters ||1'55.392||0.111|
|3||23|| Will Davison ||1'55.402||0.121|
|4||97|| Shane van Gisbergen ||1'55.503||0.222|
|5||17|| Scott McLaughlin ||1'55.854||0.573|
|6||9|| David Reynolds ||1'55.868||0.587|
|7||25|| Chaz Mostert ||1'55.902||0.621|
|8||5|| Lee Holdsworth ||1'55.992||0.711|
|9||7|| Andre Heimgartner ||1'56.069||0.788|
|10||12|| Fabian Coulthard ||1'56.091||0.811|
|View full results|