Andrea Dovizioso has claimed pole position for the Japanese MotoGP at Twin Ring Motegi denying Jack Miller in the closing stages of the session.

A late lap from the factory Ducati rider saw him demote Miller from top spot, the Australian hanging on to third after Johann Zarco banked a better lap late to secure second.

Yamaha held the top two spots early in Qualifying 2 before a flurry of activity pushed both Maverick Vinales and Valentino Rossi down the order.

For a time, Cal Crutchlow held the upper hand, pushing Marquez out of top spot with a 1:44.909s lap.

He then improved with little more than a minute remaining to record a 1:44.820 as the session built to a dramatic finale.

Cruthlow’s effort followed a lap from Marquez which had put the Honda fastest before a hail Mary lap from Jack Miller saw him take provisional pole.

It looked as though the Australian would hold on to the surprise result before Dovizisio moved beyond the fellow Ducati rider.

Zarco then pushed Miller to third as the chequered flag waved.

Andrea Iannone looked as though he might threaten Miller’s front row position but wasn’t able to produce in the final sector and instead recorded the fifth fastest time.

Miller crashed in the final moments of the session while Marquez ended up off the front row in sixth place.

Marquez had fallen in the closing moments of final practice, and was unable to remount his Honda which was left in the gravel at Turn 7.

The championship leader made it back to the pits as the session drew to a close, just moments before qualifying began, limiting him to the use of a single bike throughout the session.

From Qualifying 1, both Alvaro Bautista and Takaaki Nakagami escaped the cut to progress into the 12 rider Qualifying 2 period.

Nakagami and Danilo Petrucci held the top two spots for much of the 15-minute session, though a strong lap midway through saw Bradley Smith briefly hold a position that would see him progress.

In the closing minutes Bautista improved to sit second best only to quickly be bumped back out by Franco Morbidelli.

Smith then went fastest as the timing screens began to light up before Morbidelli fell at Turn 12 to draw the yellow flags and end his session.

Up the road, Nakagami improved to go fastest for the session just seconds before the chequered flag fell, confirming his place in the second part of qualifying along with Bautista whose last gasp lap put him to the top of the timing screens.

The Japanese MotoGP is scheduled to begin at 1600 AEDT on Sunday.

Result: Japanese MotoGP, Qualifying