Kostecki bounced back from a tough Saturday in Far North Queensland that saw him surrender his series lead to teammate Will Brown.
He did so in fine style, too, grabbing provisional pole with a rapid 1m12.838s on his final run.
That proved to be best of a flurry of improvements at the flag in what proved to be a dramatic opening session of the day.
"We made a couple of small changes and went the same direction as car #9 did yesterday and the car felt unreal as soon as I got out there," said Kostecki.
"I had a big smile on my face after the car went through turn 2 on my first lap because I knew we were on for a pretty good result. I just nailed everything. Hopefully I can replicate it in the Shootout."
Cam Waters went very close to knocking Kostecki off top spot, the Tickford driver falling just 0.08s short of the benchmark time.
He was the best of six Mustangs that made it into the Top 10 Shootout with Chaz Mostert and David Reynolds third and fourth fastest.
Jack Le Brocq easily made the Shootout with the fifth fastest time while Thomas Randle put in a smart final lap to end up sixth.
Andre Heimgartner was the only driver to not do a final run, relying on a 1m13.124s set earlier in the session to get through to the Shootout.
The plan worked, Heimgartner only shuffled back to seventh ahead of Dick Johnson Racing pair Anton De Pasqauale and Will Davison.
Race 1 winner Will Brown just snuck into the Shootout with the 10th fastest time, set in the most dramatic of circumstances.
He spent most of the session in the garage after an engine pulley broke on his first run which left him without power steering.
Erebus was able to rectify the issue and get Brown out for a single run before the flag, Brown managing to grab 10th and keep his pole hopes alive.
"On that first flying lap there the power steering went around the train tracks; I thought I was going into the fence," he said. "But we're quite lucky because what broke, if the race was two laps longer yesterday I could have lost the race."
There will be no Triple Eight cars in the Shootout with Broc Feeney only fast enough for 13th in qualifying.
Van Gisbergen, meanwhile, will start today's race from dead last on the grid after a curious session.
The Kiwi didn't set a representative time early in the session and was out of his car as the session ticked into its final few minutes.
He did get back in the car for a final run and looked on to sneak into the Shootout, only to out-brake himself into turn 10.
The first five rows of the grid will be set by the Top 10 Shootout at 12pm local time.
