Harris put down a 1:45.9894s in his Mazda, to finish 0.9037 seconds clear at the top.
Craig Woods and Tom Alexander were second and third, the same positions the Toyota and Holden drivers occupied in practice.
The Mazda team-mate of Harris, 17-year-old Aaron Cameron found the limits of his new SuperUte, hitting the tyres at the exit of Turn 3 and rolling his BT-50 onto its side.
Cameron’s crash brought out the red flag but he still wound up fourth, ahead of 2016 Dakar Rally winner Toby Price for Team Triton.
"I lost the rear of the car at Turn 4 and I tried to gather it up, but it hit the tyres at an awkward angle and rolled," Cameron told Supercars.com.
"The damage is pretty much all cosmetic so we should be right to get back out tomorrow.
"The roll cage was completely undamaged, it held up really well."
Ben Walsh (Toyota), Craig Dontas (Mitsubishi), Matthew MacKelden (Toyota) and Christopher Formosa (Ford) were sixth through to ninth.
After a delayed arrival that meant it missed practice, the Holden Colorado of Supercars outfit Team 18 finally made it out on track.
Its 15-year-old driver Tomas Gasperak completed five laps at the tail of the order.
The inaugural, eight-lap SuperUtes race will be held at 1:55pm local time on Friday.
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