There was little in the way of movement at the top of the times for much of the hour-long session, as teams focussed on race set-ups and driver changes.
That meant Shane van Gisbergen early 2m04.628s set the pace until the final five minutes, when the Top 10 Shootout simulations started.
It was at point provisional polesitter Holdsworth vaulted to P1 with a 2m04.464s.
However his stint at the top was short-lived, Waters getting the best of the quali sims with a 2m04.349s.
"There was a couple little moments, but it's just the conditions," said Waters.
"There's so much wind around it changes the car corner to corner. I think we're pretty happy and comfortable with the car. We can do the time, which is nice. We've got a bit of a vibration, I think it's in that brake package. We're just trying to work out what that is. The boys will sort it out, and obviously it's not slowing us down that much.
Chaz Mostert ended up best of the Holdens in third courtesy of a 2m04.549s on his final run, while van Gisbergen's effort was good enough to hang on to fourth.
Penske pair Scott McLaughlin and Fabian Coulthard were fifth and sixth, followed by Nick Percat in his BJR Holden.
Jamie Whincup, meanwhile was left down in eighth after making a meal of his qualifying simulation, running wide at the last corner after going purple in the first and second sectors.
"We got through our programme," said Whincup. "We did a lot of work on the race car to make it nice over a distance.
"I put some tyres on to do a Shootout simulation, but that didn't go to plan. I locked the rears and almost ran off at the last corner. But the car felt like it had grip."
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