The Kiwi was right on the pace throughout all three segments of qualifying, his fastest lap coming in Q1 when he lowered his own lap record with a 1m18.237s.
He was only fourth fastest in Q2, but ramped up the pace again in the final shootout for pole with a 1m18.264s despite a moment on the way out of the sweeper.
The margin back to Waters in second was just 0.04s.
"[The car] is better than the driver," said van Gisbergen. "I kept making mistakes and in that [segment] I had a problem, I couldn't get sixth down the straight and it hung on the limiter. I didn't lose much, but it's still annoying.
"But yeah, it's very hard to drive here. There is so much grip, the cars are really alive. I'm enjoying it. Let's see how we go in the race."
Chaz Mostert will start from third after pipping Will Brown by just 0.001s.
Lee Holdsworth, meanwhile, led the way for Grove Racing, which was surprising given teammate David Reynolds' pace in the first two segments of qualifying.
Reynolds looked well in the hunt for pole with 1m18.2s in both Q1 and Q2, before slumping to seventh behind Anton De Pasquale with a 1m18.632s when it mattered.
"I'm a bit disappointed. It was shit house," he said. "We're going to look at it, see what it is. It could be a driver fuck up. Who knows."
Broc Feeney qualified eighth ahead of Andre Heimgartner and Scott Pye.
Will Davison was the surprise omission from the final segment of qualifying after failing to get through Q2.
The Dick Johnson Racing driver was third after the first run, and then opted to sit out the second run hoping the time would be good enough to get through.
However that wasn't the case, Davison shuffled down to 13th as others improved.
"I think we were reasonable then on the first run and we would have gone a chunk quicker, but you just don't know what the track is going to do," explained Davison.
"That time we thought was going to sneak in the 10 and we knew we'd go quicker in the next segment. But what can you do? We stuffed up. We would have looked good if we got through."
Jayden Ojeda was the best of the two wildcards, the Walkinshaw Andretti United driver getting through Q1 before qualifying 19th.
Surprisingly that left him ahead of WAU teammate Nick Percat who was knocked out in the opening segment.
He will start way down in 22nd after failing to show the same sort of improvement as Mostert off the back of the team's horror show in Perth.
Tim Slade fared even worse, the Blanchard Racing Team ace only good enough for 24th on the grid.
"I would love to know," said Slade when asked post-session why he was so far back.
"I felt as though up until Perth we've had a car we could understand, things made sense. Perth was a tough one and I thought that was a one-off, but we didn't have a great test day here and that has continued in to today. No idea."
The first of three races kicks off at 3:35pm local time.
Winton SuperSprint qualifying results
| Cla | # | Driver | Car | Time | Gap | Interval |
|---|---|---|---|---|---|---|
| 1 | 97 |
 Shane van Gisbergen | Holden Commodore ZB | 1'18.264 | ||
| 2 | 6 |
 Cameron Waters | Ford Mustang GT | 1'18.306 | 0.042 | 0.042 |
| 3 | 25 |
Chaz Mostert | Holden Commodore ZB | 1'18.408 | 0.144 | 0.101 |
| 4 | 9 |
Will Brown | Holden Commodore ZB | 1'18.409 | 0.145 | 0.001 |
| 5 | 10 |
Lee Holdsworth | Ford Mustang GT | 1'18.525 | 0.261 | 0.116 |
| 6 | 11 |
Anton De Pasquale | Ford Mustang GT | 1'18.543 | 0.279 | 0.017 |
| 7 | 26 |
David Reynolds | Ford Mustang GT | 1'18.632 | 0.368 | 0.089 |
| 8 | 88 | Broc Feeney | Holden Commodore ZB | 1'18.771 | 0.507 | 0.139 |
| 9 | 8 |
Andre Heimgartner | Holden Commodore ZB | 1'18.821 | 0.557 | 0.050 |
| 10 | 20 |
Scott Pye | Holden Commodore ZB | 1'19.300 | 1.036 | 0.478 |
| 11 | 99 | Brodie Kostecki | Holden Commodore ZB | 1'18.738 | 0.473 | |
| 12 | 18 |
Mark Winterbottom | Holden Commodore ZB | 1'18.788 | 0.524 | 0.050 |
| 13 | 17 |
Will Davison | Ford Mustang GT | 1'18.793 | 0.529 | 0.005 |
| 14 | 55 |
Thomas Randle | Ford Mustang GT | 1'18.848 | 0.584 | 0.055 |
| 15 | 56 |
Jake Kostecki | Ford Mustang GT | 1'18.854 | 0.589 | 0.005 |
| 16 | 96 |
Macauley Jones | Holden Commodore ZB | 1'18.904 | 0.640 | 0.050 |
| 17 | 34 |
Jack Le Brocq | Holden Commodore ZB | 1'18.931 | 0.666 | 0.026 |
| 18 | 14 |
Bryce Fullwood | Holden Commodore ZB | 1'18.937 | 0.672 | 0.005 |
| 19 | 27 | Jayden Ojeda | Holden Commodore ZB | 1'19.056 | 0.792 | 0.119 |
| 20 | 5 |
James Courtney | Ford Mustang GT | 1'19.083 | 0.819 | 0.027 |
| 21 | 35 |
Todd Hazelwood | Holden Commodore ZB | 1'19.179 | 0.915 | 0.095 |
| 22 | 2 |
Nick Percat | Holden Commodore ZB | 1'19.181 | 0.916 | 0.001 |
| 23 | 49 | Jordan Boys | Holden Commodore ZB | 1'19.203 | 0.938 | 0.022 |
| 24 | 3 |
Tim Slade | Ford Mustang GT | 1'19.282 | 1.017 | 0.079 |
| 25 | 22 |
Chris Pither | Holden Commodore ZB | 1'19.296 | 1.031 | 0.014 |
| 26 | 4 |
Jack Smith | Holden Commodore ZB | 1'19.392 | 1.127 | 0.095 |
| 27 | 76 |
Garry Jacobson | Holden Commodore ZB | 1'19.526 | 1.261 | 0.134 |
| View full results | ||||||
