While Brown is on provisional pole, all it means is he goes out last in the Top 10 shootout and has plenty of work ahead of him.
But Brown was a happy man as he landed a massive confidence boost from the hot lap.
"I said to Tommy, 'I grew some balls out there and had a dip'. That was bloody awesome. How good was that," he said.
"To do a 2:03 round here, I didn't care if I got pole or not, that's a pretty wicked time. I'm just pumped."
Brown also revealed that his sponsor Shaw and Partners had put up $25,000 each for charity Feel The Magic if he and Brodie Kostecki got in the top 10 — Kostecki was sixth.
Asked where on the track he picked up time to pip his rivals, he said: "I don't know and I don't care. I'm just happy I'm P1 after that. Obviously it's tight up there, I'm glad I'm on the right side of that seven hundredths but it's going to be tight in the shootout. To get provisional pole at Bathurst in my first year is pretty bloody cool."
Brown added later that he believed it wasn't as good a lap as it turned out to be and was in disbelief over the result.
"It took me a second; I was looking at the last number for a two or something, and I saw an eight," Brown said.
"I thought that wasn't very good, I thought I did a 2:04.8.
"It took me a second and I worked it out. I probably then wasn't worried where I'd end up.
"I thought a 2:03 around here was pretty cool. I was happy and I knew it'd put us in the shootout.
"It's cool to be the number one man. We'll see what happens tomorrow."
While Brown was thrilled, Whincup was the opposite as he missed the shootout for the first time since 2017.
"Plenty of excuses," Whincup said.
"We didn't get green runs in practice before, they're a good opportunity to get up to speed, look at the data and work away from there.
"The car was probably good enough... disappointed with that, but what can you do? Put your head down and try to make it up in the race."
Shane van Gisbergen was the best of the Kiwis in the field in seventh place with Andre Heimgartner settling for a start in 17th and Fabien Coulthard a lowly 20th. Chris Pither, who is pairing with lead-driver Macauley Jones on Sunday, will start from 22nd on the grid.
Bathurst 1000 qualifying Top 10 results
1. Will Brown: 02:03.8989s
2. Anton de Pasquale: 02:03.9218s
3. Chaz Mostert: 02:03.9770s
4. Tim Slade: 02:04.1540s
5. Cameron Waters: 02:04.2035s
6. Brodie Kostecki: 02:04.2201s
7. Shane van Gisbergen: 02:04.2278s
8. Will Davison: 02:04.3078s
9. Nick Percat: 02:04.4421s
10. Jack le Brocq: 02:04.4933s
