Marc Marquez flew to his maiden premier class Motegi pole position; holding off both Petronas SRT Yamaha machines to complete the feat.
Conditions had improved markedly since the sodden FP3 session, with only damp patches remaining as the Q1 runners headed out on track-slicks now the order of the day.
Marquez was the favourite for pole heading into qualifying despite never having scored pole at the Japanese venue before, and looked to be living up to this promise as he held a 0.567 advantage over Jack Miller after the opening runs.
Things got juicy as the final runs began though, Marquez only going for one final flyer and improving on his benchmark by just 0.031 to set a 1:45.763 as the chequered flag came out.
Cal Crutchlow looked set to snatch an unlikely pole as he sat just over a tenth under Marquez’s time half-way round the lap, but lost out over the second part of the lap and dropped 0.426 behind Marquez come the end of the tour.
Ultimately no-one was able to knock Marquez off his perch, although the SRT squad came closest as Franco Morbidelli led Fabio Quartararo to close out the front row-just 0.132 and 0.181 away from pole respectively.
Maverick Vinales was forced to settle for fourth on the first of the factory M1’s, with Crutchlow fifth just behind.
Crutchlow topped the Q1 session held just minutes before the shootout, posting two times quick enough to lead the test.
It was local boy Takaaki Nakagami who led the opening runs though with a 1:47.877, leading Crutchlow while Alex Rins just missed out on a provisional Q2 spot with his own opening gambit.
Nakagami was on a mission as the final runs got underway, immediately banging in the first sub-47 lap of the session with a 1:46.998 to extend his leading advantage at the head of the times.
This was as good as it got though as he failed to improve further, while Crutchlow moved 0.173 clear with his penultimate flyer, extending his lead to three-tenths with his final effort.
The final punch to the stomach for Nakagami was inflicted by Rins though, who pipped him to the final Q2 spot by just 0.034 in the dying seconds, limiting him to a 13th place start in his final event of the season in front of his home fans.
Rounding out the top six on the grid meanwhile was Jack Miller on the first of the Pramac Ducati’s, with factory men Andrea Dovizioso and Danilo Petrucci-who at one point looked to be in the hunt for pole-following in seventh and eighth behind on their own Desmosedici GP19’s.
Aleix Espargaro managed a strong ninth for Aprilia, while Valentino Rossi could only come up with a slightly underwhelming tenth fastest time.
The Suzuki pairing closed out the Q2 runners, with Rins getting the best of rookie team-mate Joan Mir in the closing moments by just 0.015 to start 11th.
KTM suffered significantly throughout qualifying meanwhile despite Pol Espargaro looking like a potential Q2 threat early in the first part of qualifying, the Spaniard managing only 15th on the grid ahead of fellow RC16 riders Miguel Oliveria and Mika Kallio.
Jorge Lorenzo came up short with his own efforts, the Honda man 1.5 seconds down on Crutchlow’s Q1 benchmark that was enough for only 19th on the grid.
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