Having provisionally qualified second in the preceding two-part session, Waters was second-to-last on track in the Top 10 Shootout.
Waters went on to clock a 1:06.2529s in the #6 Tickford Racing Ford Mustang.
A meagre 0.0612s split the top two Mustangs, with the earlier pacesetter Matt Payne second for Grove Racing.
“Quali was super tricky,” said Waters.
“The car didn’t feel great, it was obviously still fast, but awesome to make it a little better in the Shootout and put a nice lap together.
“It’s been a trying year, it’s awesome to have good results and a consistent weekend so far.
Secure your spot today.
“I’ve got one more race. Hopefully we can make the car a little better in the race and get a win.”
Anton De Pasquale made headway from fifth to third in the #18 Team 18 Chevrolet Camaro, just 0.1724s away from Waters.
Triple Eight’s Broc Feeney only lost one position to fourth, bemoaning a lock-up into Turn 11.
Chaz Mostert (Walkinshaw TWG) completed the top five ahead of Will Brown (Triple Eight), Jack Le Brocq (Matt Stone Racing), Cameron Hill (Brad Jones Racing), Zach Bates (Matt Stone Racing) and Andre Heimgartner (Brad Jones Racing).
Race 3 of the Darwin Triple Crown is scheduled for 3:10pm AEST.
Results: Repco Supercars Championship betr Darwin Triple Crown, Race 3 Top 10 Shootout
| Pos | Num | Driver | Team | Car | Lap | Diff | Gap |
| 1 | 6 | Cameron Waters | Tickford Racing | Ford Mustang GT | 1:06.2529 | ||
| 2 | 19 | Matthew Payne | Grove Racing | Ford Mustang GT | 1:06.3141 | 0.0612 | 0.0612 |
| 3 | 18 | Anton De Pasquale | Team 18 | Chev Camaro ZL1 | 1:06.4253 | 0.1724 | 0.1112 |
| 4 | 88 | Broc Feeney | Triple Eight Race Engineering | Ford Mustang GT | 1:06.5618 | 0.3089 | 0.1365 |
| 5 | 1 | Chaz Mostert | Walkinshaw TWG Racing | Toyota GR Supra A90 | 1:06.5805 | 0.3276 | 0.0187 |
| 6 | 888 | William Brown | Triple Eight Race Engineering | Ford Mustang GT | 1:06.6428 | 0.3899 | 0.0623 |
| 7 | 4 | Jack Le Brocq | Matt Stone Racing | Chev Camaro ZL1 | 1:06.7886 | 0.5357 | 0.1458 |
| 8 | 14 | Cameron Hill | Brad Jones Racing | Toyota GR Supra A90 | 1:06.7937 | 0.5408 | 0.0051 |
| 9 | 10 | Zach Bates | Matt Stone Racing | Chev Camaro ZL1 | 1:06.8326 | 0.5797 | 0.0389 |
| 10 | 8 | Andre Heimgartner | Brad Jones Racing | Toyota GR Supra A90 | 1:06.9313 | 0.6784 | 0.0987 |
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