The Erebus driver was untouchable across the session, securing provisional pole by over a tenth of a second with a rapid 2m04.664s.
That means he'll run last in the Top 10 Shootout tomorrow evening, which will determine the first five rows of the grid.
It was a different story for Kostecki's closest title rival Shane van Gisbergen, who only rescued his Shootout hopes with the seventh fastest time on his very last lap.
Brown, meanwhile, missed the Shootout altogether after a difficult session that started with a trip into the turn 2 tyre wall.
Brown was responsible for a dramatic start to the 40-minute session, the title contender firing his Erebus Camaro into the wall on his first run.
That prompted an early red flag, Brown able to get the damaged car out of the tyre barrier and back to the pits to begin repairs.
After a little under 10 minutes the session went green again without a single representative time on the board.
And nobody could get a lap in before the red flag was back out, this time thanks to Fraser clouting the wall hard at The Cutting, putting him out on the spot.
The second stoppage was a blessing for Brown, giving his crew time to repair his car and send it back out just a few minutes after the next restart.
When the times did start to land they were spectacular, Cam Waters becoming the first driver into the 2m04s in a Gen3 car when he jumped to the top with a 2m04.990s.
Initially he had Matt Payne a couple of tenths behind him, before James Golding jumped into second with a 2m05.163s.
Once Kostecki finally got a lap done it was even more spectacular, the series leader charging clear out front with a 2m04.664s.
Both Golding and Anton De Pasquale were able to sneak into the 2m04s on their next runs, Kostecki continuing to hold an advantage of over a tenth of a second as the clocked ticked down.
The lead group did all head out for a final run, however there were no changes right at the top, Kostecki taking provisional pole ahead of Golding.
Golding was the surprise of the session with his second place ahead of De Pasquale and Waters.
Broc Feeney, another driver still in contention for the title, was fifth fastest while David Reynolds ended up the best of the Grove Racing cars in seventh after improving on his final lap.
Van Gisbergen spent the majority of the session outside the top 10, the Kiwi digging deep right at the flag to end up seventh, and keep his hopes of pole position alive.
That dropped fellow Kiwi Matt Payne back to eighth ahead, with Chaz Mostert and Will Davison the last two drivers to book their Shootout berth.
Brown and co-driver Jack Perkins will start Sunday's Great Race from 17th with Brown unable to crack the best 10 in his repaired car.
The 2023 Repco Bathurst 1000 continues with two more practice sessions at 10am and 1pm local time tomorrow, followed by the Top 10 Shootout at 5:05pm.
