The opening 10-minute session came down to a battle of the Tickford Mustangs between Waters and surprise contender Thomas Randle.
Waters initially got the best of the crucial final runs with a 1m48.348s, only for Randle to then go purple in the first two sectors.
The rookie fell away in the final sector, though, helping Waters hang on to pole by just 0.07s.
Race 1 winner Shane van Gisbergen, who was fastest on the first run, ended up third ahead of James Courtney, Anton De Pasquale and Chaz Mostert.
Broc Feeney and Mark Winterbottom were next, while Bryce Fullwood and Lee Holdsworth were ninth and 10th.
The surprise of the first session was an in-form Will Davison, who ended up just 23rd on the grid after locking up on his final run.
In the second session most of the fast times came on the first run, Waters sealing pole with a 1m48.337s straight out of the gate.
He did do a better first sector on his final run but, with pole secured, didn’t go on with the lap.
“It’s awesome,” said Waters. “The car is really, really nice today. A lot better than it was yesterday. It’s still not perfect, but it can’t be that bad.”
De Pasquale was second, just 0.03s slower than Waters, while van Gisbergen made it a pair of thirds.
Feeney moved up to fourth in the second session ahead of Courtney and Will Brown.
Yesterday’s shock pole winner Zak Best, now on the same tyre batch as the rest of the field, was seventh fastest in the second session, following his 16th in the first.
Randle capped off a solid morning with eighth in the second session ahead of Mostert and Davison.
The second session saw another big name at the bottom of the time sheets, David Reynolds qualifying 27th and last.
The first of today’s 120-kilometre races kicks off at 12:30pm local time.