The last to appear in the Top 10 Shootout after topping qualifying earlier in the afternoon, Waters continued his scintillating Sydney form to secure pole.
His 1:29.1362s effort put him a 0.2268s clear of Feeney, who had shot to the top as the penultimate runner.
Waters converted pole to victory in the opening race on Friday, while Feeney ended up down the order after an early puncture.
Friday podium getters Chaz Mostert and Thomas Randle will share the second row ahead of Will Brown, Matt Payne, Ryan Wood, Andre Heimgartner, Cam Hill and Bryce Fullwood.
Wood improved two positions from qualifying, holding the top spot until being knocked off by Randle, who was in turn deposed by Mostert by just 0.0009s.
Feeney went to the top despite a huge understeer moment in Turn 1 – a condition that appeared to earlier impact teammate Brown too.
Waters was subsequently two-tenths faster than Feeney to the end of the first sector, setting up his second pole position in as many days.
The 200km second race of the season will get underway at 7:30pm local time.
Results: Repco Supercars Championship Sydney 500, Top 10 Shootout Race 2
| Pos | Num | Driver | Time | Diff | Gap |
| 1 | 6 | Cameron Waters | 1:29.1362 | ||
| 2 | 88 | Broc Feeney | 1:29.3630 | 0.2268 | 0.2268 |
| 3 | 25 | Chaz Mostert | 1:29.3997 | 0.2635 | 0.0367 |
| 4 | 55 | Thomas Randle | 1:29.4006 | 0.2644 | 0.0009 |
| 5 | 1 | William Brown | 1:29.5832 | 0.447 | 0.1826 |
| 6 | 19 | Matthew Payne | 1:29.7102 | 0.574 | 0.127 |
| 7 | 2 | Ryan Wood | 1:29.7645 | 0.6283 | 0.0543 |
| 8 | 8 | Andre Heimgartner | 1:29.8846 | 0.7484 | 0.1201 |
| 9 | 4 | Cameron Hill | 1:29.8910 | 0.7548 | 0.0064 |
| 10 | 14 | Bryce Fullwood | 1:30.0573 | 0.9211 | 0.1663 |
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