The Erebus driver continued his impressive start to the Gen3 era, backing up his Friday practice-topping form with provisional pole in qualifying.
He set what proved to be an unbeatable 1m11.321s on his first run in the 20-minute session, even opting to abort his final run early.
That fastest time means he'll run last in the single-lap dash for pole position ahead of today's season-opening race.
"It's been pretty wild out there the whole weekend and the track is still trying to rubber up a little bit," said Kostecki.
"It was great to have the speed yesterday, but to carry it on today is unreal.
"We'll see how we go [in the Shootout]. The second set of tyres I put on, I didn't quite do a good job go phasing them in. I'll have to do a better job in the Shootout with that."
Chaz Mostert ended up second fastest, just three-hundredths behind Kostecki, while Shane van Gisbergen improved on his final run to slot into third.
PremiAir Racing had a solid session getting two cars into the Shootout. Tim Slade was the best of the Nulon Camaros in fourth while James Golding was 10th fastest.
David Reynolds booked his Shootout berth with the fifth quickest time had of Cam Waters and Broc Feeney.
Andre Heimgartner and Scott Pye were eighth and ninth.
Will Brown just missed out on the Shootout with the 11th fastest time, despite being less than half a second off teammate Kostecki.
Both Dick Johnson Racing Mustangs missed out too, Will Davison slumping to 14th as he battled a clutch issue.
Anton De Pasquale, meanwhile, was just 17th fastest.
Another high-profile omission was Nick Percat who qualified well behind teammate Mostert in 21st.
The battle of the rookies went to Cam Hill in 19th, with Matt Payne 22nd and Declan Fraser 24th.
