The Tickford driver timed his run to perfection, squeezing his lap right in between a mid-session red flag and a late shower of rain.
The stoppage was courtesy of Jake Kostecki firing into the wall on the way down the hill, coming right as Jamie Whincup has just gone quickest with a 2m04.266s.
Conditions actually improved as the Kostecki car was cleared, increasing cloud cover setting up a fascinating 20-minute showdown for a spot in tomorrow's Shootout.
McLaughlin swiftly lowered the benchmark to a 2m04.103s, before Shane van Gisbergen went quicker again with a 2m04.035s.
The Kiwi was then trumped by Holdsworth's 2m04.024s.
That time wasn't immediately safe, coming with plenty of time for a final run as conditions continued to cool.
But right as a number of contenders went out for one last crack the heavens opened, a burst of rain at the top of the Mountain sealing provisional pole for Holdsworth and co-driver Michael Caruso.
"I've still got the Shootout tomorrow, but this is my first provisional pole at Bathurst," said Holdsworth.
"We'll string it all together tomorrow and worry about Sunday on Sunday. I can't say enough how much [Michael] Caruso has helped me with the car this weekend."
Van Gisbergen finished up second, the gap just 0.01s, while McLaughlin finished up third, disappointed that he didn't get his final run in.
"I was rubbing my hands together, like 'let's go'," he said. "I got to McPhillamy and it was bucketing down. I went over the hill and it was loose on the slicks, so I said 'nah boys, we'll bring it in'.
"We'll have another crack tomorrow in the Shootout."
Cam Waters and Whincup finished up fourth and fifth, followed by Fabian Coulthard, Anton De Pasquale and Chaz Mostert – the latter battling a suspected coil pack issue during the session.
James Courtney was ninth fastest, while Nick Percat snuck into the Shootout with 10th despite setting his lap without a functioning shift-cut.
Bryce Fullwood was the man left on the bubble, the rookie set to start the Great Race from 11th, as the likes of David Reynolds (13th), Andre Heimgartner (14th), Mark Winterbottom (18th) and Rick Kelly (19th) all missed out on a Shootout berth.
Bathurst 1000: Qualifying results:
|1||5||Michael Caruso||Ford Mustang GT||2'04.024|
|2||97||Garth Tander||Holden Commodore ZB||2'04.035||0.010|
|3||17||Tim Slade||Ford Mustang GT||2'04.103||0.079|
|4||6||Will Davison||Ford Mustang GT||2'04.105||0.081|
|5||88||Craig Lowndes||Holden Commodore ZB||2'04.266||0.241|
|6||12||Tony D'Alberto||Ford Mustang GT||2'04.281||0.257|
|7||99||Brodie Kostecki||Holden Commodore ZB||2'04.466||0.442|
|8||25||Warren Luff||Holden Commodore ZB||2'04.493||0.469|
|9||44||Broc Feeney||Ford Mustang GT||2'04.548||0.524|
|10||8||Thomas Randle||Holden Commodore ZB||2'04.553||0.529|
|11||2||Kurt Kostecki||Holden Commodore ZB||2'04.605||0.580|
|12||20||Dean Fiore||Holden Commodore ZB||2'04.632||0.607|
|13||9||Will Brown||Holden Commodore ZB||2'04.673||0.648|
|14||7||Dylan O'Keeffe||Ford Mustang GT||2'04.853||0.828|
|15||55||James Moffat||Ford Mustang GT||2'04.905||0.881|
|16||14||Jordan Boys||Holden Commodore ZB||2'04.972||0.948|
|17||3||Tim Blanchard||Holden Commodore ZB||2'05.037||1.013|
|18||18||James Golding||Holden Commodore ZB||2'05.173||1.148|
|19||15||Dale Wood||Ford Mustang GT||2'05.259||1.234|
|20||19||Jonathon Webb||Holden Commodore ZB||2'05.332||1.307|
|21||35||David Russell||Holden Commodore ZB||2'05.414||1.389|
|22||4||Jack Perkins||Holden Commodore ZB||2'06.349||2.325|
|23||22||Steven Owen||Holden Commodore ZB||2'06.353||2.329|
|24||40||Jayden Ojeda||Holden Commodore ZB||2'06.681||2.657|
|25||34||Zane Goddard||Holden Commodore ZB||2'15.154||11.129|
|View full results|