Brad Binder climbs to second place with 10mins remaining.
Fabio Quartararo, who sprained his ankle in a heavy fall due to a front brake 'mishap', thought to mean it was sticking on, is currently 9th.
Marco Bezzecchi is setting the early pace ahead of Marc Marquez and Francesco Bagnaia.
Final practice is underway, all riders start on the hard front and soft rear tyre combination, expected to be used in this afternoon's shorter Sprint race.
Dorna's Simon Crafar, who had been sceptical of Marc Marquez leaving Honda, says he is now joining those who believe he will depart at the end of this season.
Brad Binder took the new carbon fibre KTM chassis to the top on Friday, finally beating Jorge Lorenzo's 2015 lap record. Can the South African continue that form today?
Both factory Yamahas (Fabio Quartararo and Franco Morbidelli) and factory Hondas (Marc Marquez and Joan Mir) will need to fight their way through Qualifying 1. But first, it's the 30-minute final practice.
Despite the threat of rain today, it's currently a dry morning for final MotoGP practice and qualifying at Motegi.
Here is the upcoming schedule:
10:10-10:40: MotoGP Free Practice 2
10:50-11:05: MotoGP Qualifying 1
11:15-11:30: MotoGP Qualifying 2