Two-time champion Chalmers carded a five-under 66 in his second round in Sydney, moving into the outright lead at the halfway mark.
It was Scott who took all the attention in the morning, also shooting a 66 to dispel fears he may miss the cut after opening with a 74.
Scott, the 2009 winner, sits at two under and in a tie for ninth.
Defending champion and world number one Rory McIlroy was decent once more as his two-under 69 left him a shot behind Chalmers.
But the Northern Irishman endured a rollercoaster round, holing six bogeys, six birdies and an eagle.
Chalmers was far more consistent, producing seven birdies and just two bogeys to be the man to beat.
Alongside McIlroy a shot back are three players.
Australian amateur Todd Sinnott (67) is among them, as is countryman Adam Crawford (69).
American Conrad Shindler carded a three-under 68 to also sit at four-under overall.
Jordan Spieth, the talented American ranked 14th in the world, is at three under after a 72, with Australian duo Brett Rumford (69) and Geoff Drakeford (70) also tied for sixth.
With Scott in a tie for ninth are Australians Robert Allenby (69), Rhein Gibson (70), Richard Green (71), Jake Higginbottom (69) and Rod Pampling (67).
American Jamie Lovemark broke the course record with a six-under 65 that left him in a tie for 17th.
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