Quartararo, who clinched his only Moto2 win in the same location last year and underwent arm pump surgery ahead of this weekend, beat Honda’s championship leader Marc Marquez by 0.015 seconds.
Franco Morbidelli, who had suffered a serious fall in training on Saturday morning, had dominated the first qualifying segment and took the early lead in the second quarter with 1: 39.758 minutes.
He and Quartararo had made it to a Petronas Yamaha 1-2 after the first few runs, and after the Yamaha of Vinales work was 0.001 seconds faster than Morbidelli, Quartararo lowered the benchmark to 1: 49.484 seconds.
Marquez finished second shortly thereafter, and while Quartararo fell a few hundredths behind his own benchmark on his last attempt, the reigning champion at Turn 4 had a big moment on his last attempt and had to settle for second.
Vinales secured his first front row start since Argentina in third, ahead of other Yamaha riders Morbidelli, who failed to improve in his second Q2, and Valentino Rossi.
Andrea Dovizioso improved the order at the checkered flag and finished sixth in the Ducati, just ahead of works team mate Danilo Petrucci, who was third in the order when he fell into the left-hander at Turn 5.
Suzuki’s Alex Rins, who was the fastest in practice, was another rider who regretted a crash. He fell late on the sharp left-hander of Turn 10 and took eighth place on the grid.
LCR Honda rider Cal Crutchlow, Honda rider Jorge Lorenzo, Rins’ teammate Joan Mir and Pol Espargaro’s KTM have completed a chopping job for the second quarter that was split by just 0.941 seconds.
Pramac Ducati rider Jack Miller set the first pace in the first quarter, but crashed into Turn 5 immediately afterwards.
The Aussie got back on his bike, returned to the pits and would improve his lap time on the second run, but only qualified for 14th place – one place behind rookie teammate Francesco Bagnaia on the older Desmosedici, the Italian was a tenth before advancing to Q2 at my expense.
After his impressive Friday show, LCR’s Takaaki Nakagami will only occupy 16th place on the grid, which is also beaten by Karel Abraham’s Avintia Ducati.
Aleix Espargaro qualified as Top Aprilia as April 17th. Factory team-mate Andrea Iannone was last on the starting grid – behind the team’s wildcard, Bradley Smith – after his RS-GP slowed when leaving the pit lane in the second run due to a mechanical problem.