In a qualifying session that is expected to be dominated by Yamaha, Vinales broke Jorge Lorenzo’s 2018 lap record of 1: 31.629 minutes with 1: 31.411 minutes, leading a Yamaha 1-2-3-4.
Vinales set the early pace with 1: 32.130 minutes, but this was quickly beaten by his Yamaha factory colleague Valentino Rossi.
The FP3 pacesetter held provisional pole position for 30 seconds when Quartararo finished the opening run of Q2 the fastest of all with 1: 31.791 minutes.
While the track was calm, Vinales set off for his second run and returned to the front with a time of 1: 31.787 minutes with just under five minutes to go.
When the others drove out again, Vinales returned to the pit lane for one final run on his second motorcycle while Morbidelli began lighting the timing screens.
Morbidelli shot in 1: 31.723 seconds to take provisional pole on the Yamaha “A-spec” – essentially a 2019 bike.
This was short-lived, however, as Vinales led his works team M1 in a time of 1: 31.411 minutes to take his second pole of the season and successive Saturday wins at Misano – the Spaniard detached the airbag in his leather during his lively celebrations.
Morbidelli held his second place and took his best qualifying result of the year, with Petronas Yamaha team-mate Quartararo completing the front row.
Rossi leads the second row, missing the top three by just 0.086 seconds, while the Pramac couple Jack Miller and Francesco Bagnaia parted by just 0.002 seconds to round out the top six.
Alex Rins was the best Suzuki runner in seventh place ahead of teammate Joan Mir, who ran off the track late on the Rio corner of Turn 4, while Andrea Dovizioso on the Ducati was ninth.
Johann Zarco completed the top 10 of the Avintia GP19, with Q1 graduate Pol Espargaro only finishing 11th after an early fall at Turn 15. Miguel Oliveira (Tech 3), who also got through Q1, finished 12th.
After a fall late in FP3, Pol Espargaro slipped in Q1, while his brother Aleix Espargaro on Aprilia followed him for most of the session with 1: 32.295 minutes.
However, the Aprilia rider failed to improve on that early performance and was unable to beat Oliveira as he improved the order in the closing stages.
He will start 13th after missing a place in Q2 by 0.083 seconds, while Takaaki Nakagami, the top Honda runner, on his year-old LCR bike, finished 14th amid a miserable weekend for HRC after injury His teammate Cal Crutchlow’s withdrawal lies.
Danilo Petrucci was unable to push through his works Ducati and starts in 15th place ahead of KTM’s Brad Binder and Avintia’s Tito Rabat.
The starting line-up is completed by a disappointed Iker Lecuona (Tech 3), Honda’s Stefan Bradl, Bradley Smith (Aprilia) and Alex Marquez’s sister factory team Honda.