Factory Yamaha man Vinales posted a lap of 1m45.572s at the very end of the 45-minute Friday morning session to lead Petronas rider Quartararo by 0.258s, with Franco Morbidelli a further 0.153s behind his teammate.
Vinales first hit the top of the times when he posted a 1m46.244s effort with 19 minutes to go, although that was soon beaten by newly-crowned six-time premier class champion Marc Marquez‘s best time of 1m46.035s aboard the Honda.
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Marquez’s benchmark stood until the final few minutes, as first Morbidelli broke the 1m46s barrier to record a 1m45.983s, which was soon beaten by a 1m45.987s from Vinales.
Quartararo briefly went quickest on a 1m45.830s once the checked flag fell but that was then surpassed by Vinales’ 1m45.572s.
Marquez didn’t improve in the final stages but stayed fourth, just under half a second off the pace, while Suzuki riders Alex Rins other Joan Mir were next up in fifth and sixth.
Top Ducati honors went to Jack Miller on the Pramac-run GP19, the Australian rider edging works rider Andrea Dovizioso by just 0.009s to take seventh.
Pol Espargaro (KTM) and Cal Crutchlow (LCR Honda) completed the top 10.
Valentino Rossi ended up slowest of the Yamahas, 0.848s off the pace of Vinales in 12th, although the Italian notably did not equip a new tire for his final runs.
Danilo Petrucci was one place behind on the second works Ducati.
George Lorenzo‘s Honda struggles continued as he finished the session down in 19th, 1.8s off the pace and four places behind the year-old LCR bike of Takaaki Nakagami.
Suzuki wild card Sylvain Guintoli – the only additional entry for the Japanese GP weekend – was 21st, a little over two seconds off the pace on the third GSX-RR.