Best will share the Race 2 second row with Aaron Love, who was hit off the track on Saturday by Zane Morse, who qualified fifth.
Kai Allen, who is 84 points behind Best heading into Sunday, qualified sixth ahead of Eggleston Motorsport teammate Cooper Murray and Wood’s teammate, Zach Bates.
Cameron McLeod was the first Super3 driver in 14th overall, a day after his Nissan Altima suffered a failure on the final lap of Race 2 while holding sixth position.
There were frantic scenes on the dummy grid for Tickford, with the starter motor on Vaughan’s #5 Ford Mustang failing.
Vaughan was left stranded as his rivals rolled out, but the South Australian teenager rebounded from the issue to score an unlikely pole.
“The stress levels were going through the roof, I just had to compose myself and focus on doing the lap,” he said.
Jordyn Sinni and Lochie Dalton rounded out the top 10, ahead of Jay Hanson, Nash Morris and Jack Perkins.
There was trouble for Callum Walker, who picked up a power steering issue in his ZB Commodore, consigning the former speedway racer to last on the grid.
The Super3 benchmark was McLeod’s 1:09.5473s, with Kelly Racing’s Mason Kelly, Saturday’s winner Jobe Stewart and rookie Valentino Astuti behind.
The 40-minute Race 2 will commence at 12:40pm AEST.