It marked the 2014 Bathurst winner’s 22nd career pole, and second for Walkinshaw Andretti United following his Tailem Bend breakthrough last year.
Mostert’s flyer also saw the Sandown qualifying lap record lowered, with the Holden star going below Scott McLaughlin’s 1:07.773s from 2019.
WATCH: QUALIFYING 3 HIGHLIGHTS
All told, the margin between Mostert and Tickford Racing’s Waters was a miserly 0.04s.
Qualifying for Race 3 saw the first three-part qualifying session of the season, with the first 10-minute segment of qualifying red-flagged midway through after Jack Smith fired off into the Turn 9 sandtrap.
When the session resumed, Mostert soared to the top with a 1:07.934s, ahead of Whincup, Shane van Gisbergen and Anton De Pasquale.
The second stanza saw Mostert leap to the top with a 1:07.882s, with Winterbottom just 0.06s behind.
Remarkably, positions seven through 18 were covered by 0.1s, with eight drivers in the 1:08.2s bracket.
WATCH: MOSTERT REGAINS MOJO WITH SANDOWN POLE
Of the eight drivers, seven failed to reach the top 10, with Brodie Kostecki sneaking in by just 0.01s over James Courtney.
Some key names failed to reach the final stanza, including Courtney (11th), Nick Percat (14th), David Reynolds (16th), van Gisbergen (17th), Scott Pye (18th) and Tim Slade (19th).
Ahead of the final runs in part three of the session, Waters led the way on a 1:08.13s, ahead of Kostecki, Whincup and Brown.
Mostert fired to the top on a 1:07.63s, with Waters failing to defeat his former Tickford teammate.
Whincup, who topped the morning’s first practice session, was third ahead of Winterbottom, with Jack Le Brocq impressing to fifth.
Andre Heimgartner was the meat in a Shell V-Power Racing Team sandwich, with Anton De Pasquale sixth and Will Davison eighth.
Erebus Motorsport duo Brodie Kostecki and Will Brown also wildly impressed, rounding out the top 10.
For Mostert, a first pole in six months was good reward as he searches for his first race win for WAU.
“I can’t believe it,” said Mostert, who is just 33 points off the championship lead.
“We were struggling a little bit through practice, trying to get the balance of the car.
“Credit to Adam [De Borre, race engineer] and the whole crew here at WAU.
“We worked really hard. The guys haven’t stopped, they haven’t even had a morning tea or lunch break as they normally would.
“Maybe the track just needed a year off… obviously good conditions, cold temp, but overall super stoked, the car was good."
The 36-lap Race 3 will commence at 4:45pm AEDT.
The Repco Supercars Championship field has returned to Victoria this weekend at the Penrite Oil Sandown SuperSprint. Tickets are on sale now.