Honda's Marquez takes first pole in three years at wet Japanese GP qualifying
Marquez posted a time of 1:55.214 to snatch pole on the same circuit where he claimed his last pole in 2019, as he looks to return to MotoGP's summit following a couple of years marred by injury.
The Spaniard has had persistent problems since he broke his arm at the 2020 Spanish Grand Prix and has had multiple operations since then.
He missed six rounds of the championship following the Italian Grand Prix at Mugello in May, but made his return at last week's Aragon Grand Prix after recovering from surgery on his right arm.
Pramac Ducati's Johann Zarco (32) finished second with Red Bull KTM's Brad Binder (27) completing the front row.
"I'm really happy to be in the pole position," Marquez said. "In the morning I felt really strong on the wet, and I said 'if it's wet in the afternoon, I will try'.
"It's only pole position, but in the situation we're coming from, it's really important. It's really important for me, for all the Japanese staff, it's important for our future to achieve these small targets.
"Tomorrow in dry conditions, it will be a different race, but we will celebrate today."
Aprilia Racing's Maverick Vinales (27) and Aleix Espargaro (33) finished fourth and sixth respectively, while Ducati's Francesco Bagnaia (25), who is 10 points behind Quartararo in the overall standings, endured a frustrating afternoon coming last in Q2.
Gresini Racing's Enea Bastianini (24), who won at Aragon, will start Sunday's race in 15th place after crashing out in the first part of qualifying.