It was van Gisbergen that led the way after the early runs courtesy of a 1m13.209s on his first set of green tyres.
The Kiwi then opted to sit out the rest of the session to save rubber, confident that his time was good enough to get into the Shootout.
That confidence was well-placed, however the time wasn't quite good enough for provisional pole thanks to a 1m13.086s from Waters on a second green tyre run.
Still, van Gisbergen was satisfied with his call to sit out the end of the session to give himself some strategic freedom for the Shootout.
"Only running one set of tyres is a good thing," he said.
"I feel like we're in a good place but I need to tidy up some errors. I can't switch my tyres on so [the Shootout] is going to be pretty tough. Whether we re-use the fronts so they come up easier or run four new ones... I don't know.
"Hopefully we can switch the right front on, because I get to Turn 5 and it's stone cold.
Andre Heimgartner was third fastest after running two sets of tyres, while Will Davison followed van Gisbergen's lead and only used one set as he qualified fourth.
Jack Le Brocq was a late improver to end up fifth followed by Anton De Pasquale, Chaz Mostert, Broc Feeney, Scott Pye and Tim Slade.
David Reynolds ended up on the bubble of the Shootout, missing a spot in the single-lap dash by just 0.05s.
Both Erebus cars missed the Shootout, Brodie Kostecki just 15th and Will Brown 18th.
Nick Percat's difficult run of qualifying form continued, the Walkinshaw Andretti United driver set to start this afternoon's opening race from 20th.
Lee Holdsworth was the biggest surprise, though, the Grove Racing driver just 24th fastest.
Townsville 500 qualifying results
| Cla | # | Driver | Car | Time | Gap | Interval |
|---|---|---|---|---|---|---|
| 1 | 6 |  Cameron Waters | Ford Mustang GT | 1'13.0869 | ||
| 2 | 97 |  Shane van Gisbergen | Holden Commodore ZB | 1'13.2093 | 0.1224 | 0.1224 |
| 3 | 8 | Andre Heimgartner | Holden Commodore ZB | 1'13.3026 | 0.2157 | 0.0933 |
| 4 | 17 | Will Davison | Ford Mustang GT | 1'13.3466 | 0.2597 | 0.0440 |
| 5 | 34 | Jack Le Brocq | Holden Commodore ZB | 1'13.4551 | 0.3682 | 0.1085 |
| 6 | 11 | Anton De Pasquale | Ford Mustang GT | 1'13.5034 | 0.4165 | 0.0483 |
| 7 | 25 | Chaz Mostert | Holden Commodore ZB | 1'13.5160 | 0.4291 | 0.0126 |
| 8 | 88 | Broc Feeney | Holden Commodore ZB | 1'13.5325 | 0.4456 | 0.0165 |
| 9 | 20 | Scott Pye | Holden Commodore ZB | 1'13.6047 | 0.5178 | 0.0722 |
| 10 | 3 | Tim Slade | Ford Mustang GT | 1'13.6176 | 0.5307 | 0.0129 |
| 11 | 26 | David Reynolds | Ford Mustang GT | 1'13.6618 | 0.5749 | 0.0442 |
| 12 | 55 | Thomas Randle | Ford Mustang GT | 1'13.6891 | 0.6022 | 0.0273 |
| 13 | 18 | Mark Winterbottom | Holden Commodore ZB | 1'13.7711 | 0.6842 | 0.0820 |
| 14 | 56 | Jake Kostecki | Ford Mustang GT | 1'13.7860 | 0.6991 | 0.0149 |
| 15 | 99 | Brodie Kostecki | Holden Commodore ZB | 1'13.8137 | 0.7268 | 0.0277 |
| 16 | 14 | Bryce Fullwood | Holden Commodore ZB | 1'13.8649 | 0.7780 | 0.0512 |
| 17 | 96 | Macauley Jones | Holden Commodore ZB | 1'13.9084 | 0.8215 | 0.0435 |
| 18 | 9 | Will Brown | Holden Commodore ZB | 1'13.9093 | 0.8224 | 0.0009 |
| 19 | 5 | James Courtney | Ford Mustang GT | 1'13.9369 | 0.8500 | 0.0276 |
| 20 | 2 | Nick Percat | Holden Commodore ZB | 1'13.9552 | 0.8683 | 0.0183 |
| 21 | 31 | James Golding | Holden Commodore ZB | 1'13.9744 | 0.8875 | 0.0192 |
| 22 | 35 | Todd Hazelwood | Holden Commodore ZB | 1'13.9747 | 0.8878 | 0.0003 |
| 23 | 4 | Jack Smith | Holden Commodore ZB | 1'14.0509 | 0.9640 | 0.0762 |
| 24 | 10 | Lee Holdsworth | Ford Mustang GT | 1'14.0907 | 1.0038 | 0.0398 |
| 25 | 22 | Chris Pither | Holden Commodore ZB | 1'14.1365 | 1.0496 | 0.0458 |
| View full results | ||||||
