The two-part session set the order for a Top 10 Shootout later in the day, while locking in grid positions 11 through 24.
Waters, who qualified and finished second on Friday, was eliminated in Q1 after a mistake on his crucial lap.
“I hit the wall at Turn 3 with my left-front and ruined the lap,” he reported.
“Pretty dirty on myself there, but we’ve got a fast enough car, definitely faster than P20, so I’ve got a big afternoon ahead of me.”
Others knocked out in Q1 were Jaxon Evans, Nick Percat, Richie Stanaway, James Golding and Ryan Wood, who narrowly missed out on a chance at a final lap after the chequered flag fell.
Having qualified 20th on Friday, Brown elected to run early in Q2 – allowing him a second shot if required.
Brown raised eyebrows with a 1:12.7202s – nearly four tenths quicker than Brodie Kostecki’s lap that paced Q1 – and then elected to park up.
The Triple Eight driver’s effort appeared to withstand the subsequent onslaught in the dying seconds, only for Payne to undercut it by 0.0378s on his second lap.
“We’ve been struggling a little bit with the balance on the first lap,” said Payne.
“Obviously it’s a pretty short track here so it’s a bit hard to get the tyres up for the first run.
“But it’s funny how the tyres seem to hang on for some of us for the second lap and you can still get a bit more out of it.”
James Courtney was a shock third for the Blanchard Racing Team, rebounding strongly from a tough Friday that included a clash with teammate Aaron Cameron.
A slew of Camaros followed with David Reynolds, Bryce Fullwood, Cooper Murray, Jack Le Brocq and Cooper Murray fourth through eighth.
Dick Johnson Racing duo Brodie Kostecki and Will Davison complete the Shootout field.
Friday podium finisher Anton De Pasquale was on the wrong side of the cut-off in 11th ahead of Cam Hill, Cameron, Andre Heimgartner, Thomas Randle, Kai Allen and Chaz Mostert.
Mostert’s hopes of a Shootout berth were dashed when he run off the road at Turn 7 on his final lap.
The Top 10 Shootout will take place from 12:05pm local time.
Result: Repco Supercars Championship NTI Townsville 500, Race 2 qualifying
| Pos | Num | Team/Sponsor | Driver/s | Car | Laps | Fastest | Gap | Lap |
| 1 | 19 | Penrite Racing | Matthew Payne | Ford Mustang GT | 10 | 1:12.682 | 10 | |
| 2 | 1 | Red Bull Ampol Racing | Will Brown | Chev Camaro ZL1 | 7 | 1:12.720 | 0.0378 | 7 |
| 3 | 7 | Snowy River Caravans Racing | James Courtney | Ford Mustang GT | 10 | 1:12.883 | 0.2008 | 10 |
| 4 | 20 | TRADIE Energy | David Reynolds | Chev Camaro ZL1 | 10 | 1:12.916 | 0.2340 | 10 |
| 5 | 14 | Middy’s Racing | Bryce Fullwood | Chev Camaro ZL1 | 12 | 1:12.925 | 0.2426 | 11 |
| 6 | 99 | Erebus Motorsport | Cooper Murray | Chev Camaro ZL1 | 9 | 1:12.926 | 0.2435 | 9 |
| 7 | 9 | Tyrepower Racing | Jack Le Brocq | Chev Camaro ZL1 | 8 | 1:12.981 | 0.2985 | 8 |
| 8 | 88 | Red Bull Ampol Racing | Broc Feeney | Chev Camaro ZL1 | 10 | 1:12.991 | 0.3082 | 10 |
| 9 | 38 | Shell V-Power Racing Team | Brodie Kostecki | Ford Mustang GT | 7 | 1:13.037 | 0.3543 | 7 |
| 10 | 17 | Shell V-Power Racing Team | Will Davison | Ford Mustang GT | 11 | 1:13.046 | 0.3634 | 11 |
| 11 | 18 | DEWALT Racing | Anton De Pasquale | Chev Camaro ZL1 | 11 | 1:13.106 | 0.4236 | 11 |
| 12 | 4 | Supaglass Racing | Cameron Hill | Chev Camaro ZL1 | 12 | 1:13.191 | 0.5090 | 11 |
| 13 | 3 | CoolDrive Auto Parts Racing | Aaron Cameron | Ford Mustang GT | 8 | 1:13.219 | 0.5367 | 7 |
| 14 | 8 | R&J Batteries Racing | Andre Heimgartner | Chev Camaro ZL1 | 11 | 1:13.230 | 0.5476 | 11 |
| 15 | 55 | Monster Castrol Racing | Thomas Randle | Ford Mustang GT | 11 | 1:13.247 | 0.5647 | 11 |
| 16 | 26 | Penrite Racing | Kai Allen | Ford Mustang GT | 10 | 1:13.259 | 0.5765 | 10 |
| 17 | 25 | Mobil1 Optus Racing | Chaz Mostert | Ford Mustang GT | 10 | 1:13.370 | 0.6871 | 10 |
| 18 | 96 | Pizza Hut Racing | Macauley Jones | Chev Camaro ZL1 | 12 | 1:13.609 | 0.9263 | 11 |
| 19 | 12 | SCT Motorsport | Jaxon Evans | Chev Camaro ZL1 | 5 | 1:13.662 | 0.9795 | 5 |
| 20 | 10 | Bendix Racing | Nick Percat | Chev Camaro ZL1 | 5 | 1:13.666 | 0.9841 | 5 |
| 21 | 6 | Monster Castrol Racing | Cam Waters | Ford Mustang GT | 5 | 1:13.710 | 1.0274 | 5 |
| 22 | 62 | PremiAir Racing | Richie Stanaway | Chev Camaro ZL1 | 5 | 1:13.861 | 1.1782 | 5 |
| 23 | 31 | PremiAir Racing | James Golding | Chev Camaro ZL1 | 5 | 1:13.996 | 1.3135 | 5 |
| 24 | 2 | Mobil1 Truck Assist Racing | Ryan Wood | Ford Mustang GT | 5 | 1:15.272 | 2.5900 | 5 |












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