Waters will start 10th and third for the two sprints, having hit come across Dick Johnson Racing drivers at Turn 6 in both sessions.
The #6 Monster Mustang made nose-to-tail contact with Anton De Pasquale in the first session, and remonstrated over the radio.
In the second session, Waters caught Will Davison, and the two Mustangs made side-to-side contact.
Waters was unable to improve, with Davison qualifying 24th, seven positions behind De Pasquale. Earlier, Davison and De Pasquale qualified seventh and 19th.
It did little to deter Kostecki, who finished 23rd on Saturday after a run-in with Waters in Race 10.
Shane van Gisbergen was 11th and ninth in the two qualifying sessions, and is Kostecki’s closest rival in the championship heading into Sunday.
"Will was quite strong yesterday, and was able to manage the pace quite well," the points leader said.
"Our race cars will go quite well, I was pretty confident in practice.
"We'll hopefully get off the start-line first, and hopefully get through the hairpin this time."
Kostecki headed an all-Chevrolet top six in the first session, with Thomas Randle (#55 Castrol Mustang) quickest after the first flyers in the Race 11 session.
Kostecki (#99 Coca-Cola Camaro) moved the benchmark to a 51.3038s, before Waters (#6 Monster Mustang) dropped in a 51.2172s.
Van Gisbergen (#97 Red Bull Ampol Camaro) improved to seventh before he locked a brake at Turn 6, and ended up 11th.
Randle vaulted to the top with a 51.1003s and a 51.0883s on consecutive laps, and appeared on course for a maiden pole position.
The 25-car field rolled out for their final runs, and Davison (#17 Shell V-Power Mustang) fired the first shot with a 51.0442s.
Brown went quicker with a 50.8963s, before Kostecki went fastest of all with a 50.8335s.
Feeney (#88 Red Bull Ampol Camaro) split the Coca-Cola Camaros teammates with a 50.8364s, with Waters undone by the De Pasquale incident.
Waters improved to a 51.0744s, but was 10th all told behind Kostecki, Feeney, Brown, Matt Stone Racing teammates Jack Le Brocq and Cameron Hill, James Golding (#31 Nulon Camaro), Davison, Randle and David Reynolds (#26 Penrite Mustang).
Cars rolled out for Race 12 qualifying shortly afterwards, and Andre Heimgartner — who was 21st in the first session — set the early pace with a 51.0667s.
The Heimgartner (#8 R&J Batteries Camaro) time was the benchmark after the majority of the opening runs, before Randle again bolted into provisional pole position with a 50.8426s.
Randle’s time came without a slipstream — all the while, a back straight tailwind had turned into a headwind.
As Randle hopped out of his #55 Mustang, the other 24 drivers went out for their final runs.
Brown jumped to the top with a 50.6401s, before Kostecki fired to the top with a 50.6218s. Waters was third with a 50.6537s.
Waters was fastest to the second sector as he sat behind Davison, but was forced to make a pass and clattered into the #17 Mustang at Turn 6.
He still managed to record a 50.6993s, and will share the second row with Le Brocq (#34 Truck Assist Camaro).
Tim Slade (#23 Nulon Camaro), Feeney, Hill (#35 Truck Assist Camaro), Randle, van Gisbergen, and Mark Winterbottom (#18 DEWALT Camaro) rounded out the top 10.
Winterbottom managed 10th despite spinning between Turns 1 and 2 at the end of the session.
Chaz Mostert (#25 Mobil 1 Optus Mustang), who retired from Saturday’s race, was 13th and 11th in both sessions.
Race 11 will commence at 1:05pm local time, followed by Race 12 at 3:50pm.