Pedro Acosta slots into second place, while Bagnaia runs wide on his final lap.
Drama! Title leader Jorge Martin crashes at Turn 9, that's session over, he's only 9th and it could get worse...
Bagnaia briefly takes pole position, but future team-mate Marc Marquez goes 0.396s better for a new all-time lap record!
2mins remaining, but that will be hard to beat.
After complaining about a lack of grip on his first rear tyre, Bagnaia proves his point by snatching 2nd place with 4mins remaining.
6mins to go and Bagnaia is still 12th and last while Acosta holds pole from Bastianini and Bezzecchi.
Marc Marquez slashes 1.6s from his opening lap to push pole away from new nearest rival Pedro Acosta.
Bagnaia abandons his run and pits for a new tyre, luckily for the Italian the rain looks to have stopped.
Meanwhile, Martin barges into the side of Alex Marquez at the apex of Turn 10, both stay on board.
Marc Marquez sets a 1m 45.744s, that's two-seconds slower than Morbidelli in Qualifying 1, but good enough to hold provisional pole.
But the Gresini rider is clearly pushing on the limit and suffers a scare a few turns later.
Meanwhile, Bagnaia's cautious opening lap has left him in 12th and last.
Alex Marquez also overtakes Bagnaia early in the first flying lap, the world champion doesn't look too comfortable and is also passed by title rival Jorge Martin.
Marc Marquez spots the danger and, rather following Bagnaia as usual, overtakes the red machine on the back straight to be the first to start a flying lap.
Qualifying 2 is underway - but the rain looks to be increasing!
More rain flags are waving and the fans are starting to put on coats and raise umbrellas.
The raindrops haven't worsened, but riders will be keen to set a good early lap in Qualifying 2 just in case.
Qualifying 2 line-up:
Brad BINDER
Marc MARQUEZ
Jorge MARTIN
Pedro ACOSTA
Enea BASTIANINI
Maverick VIÑALES
Francesco BAGNAIA
Alex MARQUEZ
Fabio DI GIANNANTONIO
Marco BEZZECCHI
+ Franco MORBIDELLI, Fabio QUARTARARO
Superb effort by Quartararo, whose Yamaha team-mate Alex Rins is only 9th in Qualifying 1 (and starting 19th on the grid).
Miller pounds the tank of his KTM in frustration.
Home star Takaaki Nakagami will line-up just 21st.
Jorge Martin is out in pit lane to check the rain drops ahead of Qualifying 2...
Franco Morbidelli and Fabio Quartararo surge to the top at the end of Qualifying 1, bumping Raul Fernandez and Jack Miller out of Qualifying 2.
A group of riders were parked up waiting for a tow, Miller guns it with Augusto Fernandez, Joan Mir and Lorenzo Savadori in tow.
Replays show not only a vapour trail from Miller's KTM on the straight, rival team aerodynamicists will be interested in that, but massive rear chatter for the Australian at the following corner.
The RC16 was shaking so much it almost looked like a flat tyre (but wasn't). Miller has spoken about it all year but that's the first time we've seen the full extent of the vibration caught on camera.
The riders defy the raindrops, Miller clipping a tenth off his best time to stay on top with Raul Fernandez now in second for Trackhouse.
That's the opening run over, time for a tyre change and then hope the rain doesn't increase.
Jack Miller leads with a 1m 44.432, one-second off team-mate Brad Binder's Friday best.
Aleix Espargaro slots into second.
Let's see if they can get another flying lap or if the rain will increase...
Riders are halfway around their first flying lap, which could be their best of Qualifying 1.
3mins into Qualifying 1 and rain is being reported in pit lane!
Qualifying 1 begins...
The rain threat means riders are sure to go flat out from their first lap.
Dorna's Matt Birt says rain is expected at Motegi in 15mins, right in the middle of qualifying.
Qualifying 1 line-up:
Jack MILLER
Takaaki NAKAGAMI
Franco MORBIDELLI
Fabio QUARTARARO
Aleix ESPARGARO
Joan MIR
Johann ZARCO
Raul FERNANDEZ
Augusto FERNANDEZ
Alex RINS
Luca MARINI
Lorenzo SAVADORI
Remy GARDNER