His 1min 20.5353sec lap edged out Holden Racing Team's Garth Tander, who will start alongside him on the grid.
Ford's Mark Winterbottom was third fastest, with Lowndes fourth.
A massive crash involving Holden drivers Greg Murphy and Jonathon Webb marred the session.
Murphy rear-ended Webb at speed, destroying both cars and leaving both highly unlikely to line up in Sunday's race.
And HRT driver James Courtney's wretched weekend continued.
Despite his team working overnight to fix a car badly damaged in a Saturday smash, the 2010 champion was unable to complete a lap during qualifying - his car stopping midway through his first lap.
He will start from the rear of the grid.