Both Red Bull Holden Racing Team Commodores failed to reach the final phase of the session, Shane van Gisbergen and Jamie Whincup to start 12th and 14th.
Waters led the way after the first runs in Q3, his 54.7123s set moments after McLaughlin recorded a 54.7742s.
The Tickford Falcon of Waters and Brad Jones Racing’s Tim Slade - third at the time - opted against a second run late in the 10 minutes.
McLaughlin pounced while they watched on, setting the fastest time for the weekend, his 54.6397s good enough for the Kiwi’s 38th Supercars pole.
"That one, I absolutely made a meal of it," McLaughlin said.
"I didn’t give myself a big enough kick up the backside after practice, I need to go back and look at it.
"I’m a bit annoyed with myself. I feel like I could have done that one the first set, but anyway, it’s good for the team, we’re third and first."
Waters kept second, while McLaughlin’s Shell Ford team-mate Fabian Coulthard grabbed third and Mark Winterbottom completed an all-Ford first two rows, separated by less than one tenth.
“I’m absolutely rapt with that. We were pretty good yesterday in practice and made the car a bit better overnight,” Waters said.
“I thought that lap was pretty maxed out, I didn’t think it had anything left in it, but obviously Scotty got me at the end.
“But we’re rapt. It’s been a big turnaround, the last two events we’ve struggled, so this is really good for the Tickford guys.”
Slade was the top Holden, albeit demoted to fifth, while Chaz Mostert joined Tickford team-mates Waters and Winterbottom in the top six.
David Reynolds, Craig Lowndes, Anton De Pasquale and Will Davison completed the top 10, Davison deciding against running in the final phase.
“We had a plan and if we had to use that extra set of tyres to get in the 10, there’s no way I was going to risk putting a second heat cycle on those tyres, knowing the majority in front had new tyres,” Davison said.
“It’s frustrating, because we actually got the car really hooked up in that second segment, got through really comfortably, it’s just we paid the price for missing the boat a bit yesterday [and had to go through Q1].”