The 2022 St Petersburg pole-sitter was the only Team Penske driver to make it through to the final phase of Qualifying, when he hit the wall exiting Turn 10.
McLaughlin had done likewise a day earlier in Practice 1 but, unlike then, he was unable to catch the #3 Chevrolet when he arrived at the Turn 11/Turn 12 dogleg.
Instead, the New Zealander broke into a spin and while he escaped further damage before coming to rest at the edge of Turn 13, he stalled and triggered a red flag.
As such, McLaughlin was not allowed to continue, although it is likely that he had presumably damaged a toe link anyway.
“Overall, not a bad day for us in the Dex Imaging Chevy,” he said.
“We beat our team-mates in qualifying, which is your first job, and then we ended up P6 after our spin.
“I felt like we had a car for pole today, which was really disappointing that I made a mistake.
“I hit the wall at Turn 10 on my first out lap and bent it and spun, so unfortunately, it caused a red, took us out of qualifying, but we'll be okay for tomorrow and we can definitely work from there.”
The McLaughlin incident caused the second red flag of the Fast Six but, with neither he nor Kyle Kirkwood officially registering a time for that segment, they reverted to their Round 2 efforts.
As such, Kirkwood gets fifth on the grid, with the #3 Penske entry alongside.
Will Power is set to start 10th in the #12 Penske Chevrolet after getting caught out by the windy conditions, while team-mate Josef Newgarden could only manage 14th on the grid having failed to advance from Round 1.
Tomorrow, the Warmup takes place at 09:00 ET/ 01:00 AEDT, followed by the 100-lap Race at 12:20 ET/04:20 AEDT.
Both sessions are live and ad-free on Stan Sport, with coverage of the race beginning at 04:00 AEDT.