Whincup, who topped the timesheets in Friday's practice, was again the dominant driver at Homebush on Saturday, clocking 1 minute, 27.38 seconds and will start from the front of the grid for the top-10 shootout.
The Red Bull driver's time at the street circuit breaks the lap record set by Will Davison back in 2011.
It is just the start to the weekend Whincup wanted as he chases his fifth championship.
He currently leads team-mate Craig Lowndes by 20 points in the standings, with Lowndes qualifying fifth for Saturday afternoon's race.
Fellow contender Mark Winterbottom will start from seventh in his Ford, while the last of the title contenders Davison is the best placed of the hopefuls, in third behind Shane Van Gisbergen.
There was no shortage of drama during the 20-minute qualifying run, with Garth Tander forcing a red flag after slamming into the tyre wall and concrete barrier just moments after posting the day's fastest lap.
But that time was eventually rubbed out after the Holden driver failed to complete the session due to damage of his front-end.
Frenchman Alex Premat was involved in an incident with James Moffat as the chequered flag came out, spinning out near the finish line.
Davison also ended the session with severe damage after crashing into a tyre wall just before the chequered flag dropped.
The top-10 shootout, which determines the front of the grid for Saturday's twilight race, begins at 2.05pm (AEDT).
Jamie Whincup dominates V8 qualifying
