Vinales had the worst weekend of his MotoGP career last time in Germany when he qualified 21st and finished last, but recovered strongly and took his first pole in 2021 with just 0.071 seconds.
Vinales set the early benchmark with 1: 32.413 minutes, with Q1 pacesetters Johann Zarco and Pol Espargaro on the Honda falling behind the Yamaha rider.
While Vinales got out for the pit lane after this lap, team-mate Quartararo was ahead with 1: 32.336 minutes before he started to illuminate the timing screens on his second flyer.
Quartararo blew the field as he entered the last sector and set an all-time lap record in Assen of 1: 31.922 minutes on that lap, 0.491 seconds ahead of Vinales.
On the first flying lap of his second run, Vinales put Quartararo’s time under pressure, but made a mistake in De Bult’s left turn and lost the lap.
He didn’t make such mistakes on his follow-up tour, however, digging deep to find a 1: 31.814 minute to wrest the provisional pole from Quartararo.
Quartararo came through the first two sectors of his last lap ahead of his team-mate, but he also made a mistake on Mandeven right at Turn 10 and had to be content with the second – he left Vinales to take his first pole since the Emilia Romagna GP to celebrate last year with a new lap record.
Francesco Bagnaia jumped to third place after his death on his factory Ducati, leading LCR’s Takaaki Nakagami and Zarco.
Miguel Oliveira briefly held a front row seat in the closing stages of Q2 but was pushed back to sixth place on his KTM ahead of Alex Rins, the Suzuki rider who ultimately crashed in Stekkenval.
Jack Miller starts on the other factory Ducati in eighth place ahead of Aleix Espargaro’s Aprilia, with world champion Joan Mir on the Suzuki, Hondas Pol Espargaro and Valentino Rossi (Petronas SRT) completing the top 12.
Tech 3’s Iker Lecuona looked like he would make it into Q2 for the first time in 2021 after finishing second behind Bagnaia on the checkered flag.
But Zarco denied his death after narrowly hitting the checkered flag to take another lap, and ousted Lecuona offline on the 13th.
Lorenzo Savadori will start in 15th place on his Aprilia ahead of Alex Marquez on the LCR Honda, while his brother Marc will start in 20th place on the factory Honda.
The six-time MotoGP World Champion fell while chasing Lecuona in De Bult’s left turn on his final flying lap.
The Avintia duo Luca Marini and Enea Bastianini took the Tech 3 KTM sister of Danilo Petrucci in 17th, 18th and 19th place.