Pole seemed ready to head to Marc Marquez as there were rain spots on the final stages, but the top six switched right after death when a number of riders found lap time in the conditions.
Meanwhile, Q1 claimed several big rackets including championship leader Francesco Bagnaia and the Suzuki duo Joan Mir and Alex Rins.
The first quarter ended with wet tires, but the track was dry enough at the start of the pole shootout session to prompt the Petronas SRT duo of Valentino Rossi and Franco Morbidelli to start immediately on slicks.
But the gamble failed for Rossi when he backfired as a high-high-side on the final corner on a lap that got him on the stack early, sending him into the gravel.
At the same time, Ducati’s Jack Miller lit up the timing screens after switching to slicks shortly before to take the top of the stack at 1: 35.472 seconds, which he improved to 1: 34.374 seconds the next time around.
Johann Zarco on the Pramac Ducati set the first session benchmark for wet tires and returned to the top with slicks five minutes before the end with a time of 1: 34.211 minutes.
That only lasted seconds, however, as Honda’s Pol Espargaro flashed this with a time of 1: 33.150 minutes before Honda teammate Marc Marquez shot to the top of the pile with a time of 1: 33.037 minutes.
As Marquez drove that lap, yellow flags were displayed in the third sector for a crash by KTM’s Miguel Oliveira while the rain was falling in the first sector.
This seemed to put Marquez in an impressive first pole position since 2019, leading a Honda 1-2-3 from Takaaki Nakagami and Espargaro from LCR.
But conditions cleared enough after death and the timing screens began to glow again, with Maverick Vinales becoming the first to break Honda hearts with a time of 1: 32.681 minutes.
Quartararo, however, went after him even faster, finding 0.081 seconds to snap his third straight pole of 2021.
Miller ended up finding a time of 1: 32.704 minutes to complete the front row ahead of Morbidelli and Zarco, while Marquez was shuffled back to sixth at the checkered flag.
Nakagami leads the third row in seventh ahead of Espargaro, who crashed in a short lap at the end. Rossi will start in ninth place.
Oliveira’s late fall put him in tenth place ahead of surprising Q1 graduate Lorenzo Savadori on the Aprilia and Avintia rookie Luca Marini, who followed Savadori in the first quarter.
Aleix Espargaro via sister Aprilia took the lead just seconds from the checkered flag but prematurely celebrated his efforts and was surprised by the late improvements for teammates Savadori and Marini.
Espargaro starts 13th ahead of the Suzuki duo of world champions Mir and Rins, who both set the Q1 pace in the first half of the training session.
Championship leader Bagnaia added to his name the list of high profile drivers who couldn’t escape the first quarter. The Ducati rider was only able to finish 16th ahead of 2020 Le Mans winner Petrucci.
His Tech 3 KTM team-mate Iker Lecuona will start in 18th place ahead of Alex Marquez of LCR, who crashed late, and Pramacs Tito Rabat in 20th place.
Brad Binder’s miserable weekend at Le Mans continued into the first quarter. The KTM rider started 21st ahead of only Avintia newcomer Enea Bastianini.