The Honda rider was over a second clear of the field after Friday’s practices, and duly delivered on his status as favourite for his ninth pole of the year ahead of his 200th grand prix start with a blistering final effort of 1m47.009s.
It was Q1 pacesetter Franco Morbidelli who set the initial pace in Q2 aboard the Petronas Yamaha, before being demoted by Pramac Ducati’s Jack Miller and the works Yamaha of Maverick Vinales.
Miller bettered Vinales’s 1m48.159s on his follow-up tour with a 1m47.862s, with Quartararo on the sister Petronas bike soon edging ahead.
However, their laptimes paled into insignificance as Marquez put in his first flying lap of 1m47.050s to go almost eight tenths clear of the field.
The reigning champion managed to go slightly quicker on his last effort with a 1m47.009s.
But Quartararo, who battled hard with Marquez for victory at Misano, came through the first two sectors fastest of all and held a slight advantage as he came through the third sector.
He couldn’t hold that slender lead, however, and missed out on pole by 0.327s to take second.
This demoted Vinales to third and Miller off the front row, while Aleix Espargaro shadowed Marquez to secure Aprilia’s first top five qualifying result since last year’s Catalan GP.
Valentino Rossi completes row two on the sister works Yamaha ahead of LCR Honda’s Cal Crutchlow, Morbidelli, Joan Mir (Suzuki) and Andrea Dovizioso (Ducati).
Andrea Iannone ensured two Aprilias would make it into Q2 for the first time since the split qualifying format was introduced. He was last of the 11 runners present in Q2, as Pol Espargaro has been forced to sit out the rest of the weekend after fracturing his left wrist.
Q1: Rins, Petrucci eliminated
Alex Rins was the big-name scalp in Q1, the Suzuki rider missing out on a place inside the pole shootout by just over a tenth of a second.
He attempted to replicate the strategy teammate Mir used on Friday to secure a Q2 berth in FP2 in using the hard rear tyre for his final run, but came up short with a 1m48.449s.
LCR’s Takaaki Nakagami shadowed him in 14th ahead of the works Ducati of Danilo Petrucci and his Pramac counterpart Francesco Bagnaia.
Johann Zarco’s KTM replacement Mika Kallio held fifth for much of the session, but was dropped back to ninth in the end.
He will start his first race since last year’s Catalan GP in 19th, having outpaced Honda’s Jorge Lorenzo by two tenths.