However the team needn't have worried, with Vilander eventually beating Mostert's best time by almost two tenths, via a 2:02.861.
"The lap was pretty good. I had a little moment at the last corner, I'm really not sure why - maybe there was some dirt," said Vilander.
"It's not an easy format of qualifying. In the shootout there's some extra pressure. You wait three long hours to get out there, and you really don't know what to expect.
"The track itself is awesome, one of the best in the world. It's cool to be back here.
"I'm really happy, happy to be with these two legends here [Craig Lowndes and Jamie Whincup], so we're looking strong for tomorrow."
Adding to the occasion was that the trophy for pole position, dedicated to the memory of the late Allan Simonsen, was won by his old team. Vilander knew Simonsen and often raced against him, making the award extra significant.
"I saw Allan [Simonsen] for the first time in 94, when I raced in Denmark. I even raced when he had the big accident, I had talked to him on the grid," said Vilander.
Expat New Zealander Steve Richards, co-driver to Marco Wittman and Mark Winterbottom, starts from third place on the grid - just reward after his BMW Team SRM team endured a difficult debut 2016 season in the Australian GT Championship.
The on-track success comes after a recent test day for the BMW squad at Bathurst, as well as technical upgrades that have helped make the platform more competitive.
"The preparations have been great. I think for us to have two BMW M6 GT3s in the top three is something fantastic," said Richards.
"Let's face it, we, and I suppose some of the other manufacturers, were a few years behind the eight ball. So the opportunity to come up here and do the test day in November with the cars, that's been a huge benefit to us, and also to have the support of BMW Motorsport is reflective of where we are on the grid."
Beyond the top three, the best of the rest was the surprise package of Miedecke Stone Motorsport and their Aston Martin V12 Vantage GT3.
With ex-Supercars Championship driver Ash Walsh behind the wheel, the team - which also consists of George Miedecke and Tony Bates - qualified in eighth place for the shootout. They then vaulted up through the order during the shootout to take fourth.
Behind Richards, the best New Zealander in the order is Earl Bamber. The Porsche factory driver qualified in seventh in the shootout; losing some time at the final corner after running wide.
It was a mixed day for the New Zealand contingent - punctuated by STM Mercedes-AMG drivers Shane van Gisbergen and Craig Baird's poor run through qualifying.
Touted as a favourite for outright contention, the team and fellow co-driver Maro Engel appeared to struggle in qualifying. With a poorly timed red flag also failing to help their cause they eventually qualified 18th, behind fellow Kiwis Daniel Gaunt and Matt Halliday, who share an Audi R8 with Ash Samadi.
Technical dramas also stunted the charge of Dominic Storey, with he and co-drivers David Reynolds and Mark Griffith getting denied the full period of time in qualifying thanks to time spent in the pits. They will start tomorrow's race from 23rd, one spot ahead of Simon Evans in 24th in his GT3 debut, and four spots behind fellow GT3 debutant Andrew Waite.
Chris Pither will start from 26th in his Am Hobson Motorsport Nissan Nismo R35 GT-R, defending Eneos Oils North Island Endurance Series champion Sam Fillmore starts from 30th, and the Kiwi Racing quartet of Glenn Smith, John De Veth, Kevin Bell, and Nick Chester start 38th.
