Matt Payne, who was fastest in the preceding qualifying session, couldn’t convert provisional pole into top spot and was only third in the Grove Racing Ford Mustang.
Waters will line up alongside Dick Johnson Racing’s Brodie Kostecki, who also improved one place on the previous session.
The top two Mustangs were split by 0.2090s.
“It’s awesome to get the pole. I probably should have got one on Friday but I made a bit of a mistake,” said Waters..
“It was awesome to do a nice, clean lap there. That’s the best the car has felt.
“Middle sector has been pretty good all weekend. We got through Turn 2 and 3 not too bad and I knew I just had to keep my strengths from there.
Secure your spot today.
“You kind of know once you get up a little bit, you’ve got good grip and you keep pushing harder and harder.”
Ryan Wood made session-on-session gains from seventh to fourth for Walkinshaw TWG Racing. Grove Racing’s Kai Allen also made major gains from 10th to fifth.
The Top 10 Shootout was rounded out by Chaz Mostert (Walkinshaw TWG), Broc Feeney (Triple Eight), Thomas Randle (Tickford Racing), Andre Heimgartner (Brad Jones Racing), and Jayden Ojeda (PremiAir Racing).
Race 3 of the Townsville 500 gets underway at 3:05pm AEST.
Results: Repco Supercars Championship NTI Townsville 500, Race 3 Top 10 Shootout
| Pos | Num | Driver | Team | Car | Lap | Diff | Gap |
| 1 | 6 | Cameron Waters | Tickford Racing | Ford Mustang GT | 1:12.5644 | ||
| 2 | 17 | Brodie Kostecki | Dick Johnson Racing | Ford Mustang GT | 1:12.7734 | 0.209 | 0.209 |
| 3 | 19 | Matthew Payne | Grove Racing | Ford Mustang GT | 1:12.8336 | 0.2692 | 0.0602 |
| 4 | 2 | Ryan Wood | Walkinshaw TWG Racing | Toyota GR Supra A90 | 1:12.8404 | 0.276 | 0.0068 |
| 5 | 26 | Kai Allen | Grove Racing | Ford Mustang GT | 1:12.8873 | 0.3229 | 0.0469 |
| 6 | 1 | Chaz Mostert | Walkinshaw TWG Racing | Toyota GR Supra A90 | 1:12.9083 | 0.3439 | 0.021 |
| 7 | 88 | Broc Feeney | Triple Eight Race Engineering | Ford Mustang GT | 1:12.9382 | 0.3738 | 0.0299 |
| 8 | 55 | Thomas Randle | Tickford Racing | Ford Mustang GT | 1:12.9865 | 0.4221 | 0.0483 |
| 9 | 8 | Andre Heimgartner | Brad Jones Racing | Toyota GR Supra A90 | 1:13.4004 | 0.836 | 0.4139 |
| 10 | 31 | Jayden Ojeda | PremiAir Racing | Chev Camaro ZL1 | 1:13.5278 | 0.9634 | 0.1274 |
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