Brad Binder put in a performance worthy of a champion as he held his nerve to put in the fastest lap of the session after the chequered flag in a massive dash for pole after a red flag delay.
The Red Bull KTM Ajo rider found enough track space to set a best of 1m 37.696, which was 0.094 ahead of his nearest rival after getting the best of the cold, windy conditions after the rain finally left the circuit after an early shower.
Fabio Quartararo was hot on his heels for second after also finding a way through the traffic for Leopard racing.
Nicolo Bulega scaled his way back to third for an all KTM front row after an eventful session. The rookie had looked ready to storm to the top of the timesheets before being forced out wide by a slowing Francesco Bagnaia on track, his quick reactions saw him avoid a horror crash and almost save his Sky Racing VR46 machine, riding sideways through the gravel before finally falling at the barrier with nowhere else to go. The red flag gave him time to regroup and have his bike fixed, and he took the opportunity to score a front row start.
Gabriel Rodrigo had his best qualifying performance to date as he too made the best of the difficult session to take fourth for RBA Racing, ahead of Peugeot man John McPhee, who was on pole last year after Danny Kent was penalised, he lead the session briefly for the Saxoprint team on his way to fifth on the grid.
Livio Loi's late dash pulled him up to sixth for RW Racing, to complete the second row.
Andrea Migno put two Sky Racing bikes into the top ten by securing seventh, with Darryn Binder alongside him after eclipsing his previous best grid placing of 16th with a superb eighth for Platinum Bay Real Estate. He will be the top Mahindra on the grid.
Jorge Martin had also been in contention for pole early on before being shuffled down to ninth in the closing rush for Aspar Mahindra, while his team-mate Bagnaia completed the top ten.
Niccolo Antonelli was the first to fall as all the riders tried to fit in a first lap on slicks before the rain returned for an early shower, leaving the unlucky Italian with a wait as his mechanics got to work in the pits.
On his return to track his bad day got much worse, he was pictured pushing his bike through the grass, having seemingly had a technical issue on his return, leaving him with no time set until the final dash where he found enough for 19th.
Phillip Oettl had been the first rider out on slicks and after immediately being fastest by over two seconds lost his advantage in the restart to drop to 20th at the flag for Schedl GP Racing.
Albert Arenas then lost the front at turn eleven with just under twenty minutes remaining. Juanftran Guevara had been running at pole pace before being tossed from his bike at turn twelve, causing a red flag as he required treatment at the scene, before being stretchered away, he was conscious but taken to the medical centre by ambulance where he was treated for chest and abdomen trauma.
Andrea Locatelli only lasted until turn four on the restart as he found himself out wide on the slippery white line looking for space, he was quickly joined by Aron Canet who had an off on turn one after waiting to exit to try to find a gap. Hiroki Ono also tripped himself up on the restart.
Matt Barton (Suus Honda - FTR)was awarded a wild-card entry again this year but was slowest in the very difficult conditions at his home circuit.