Going without a win since last year’s wet French GP, Miller grabbed the lead on lap three and streaked away to his first victory of the season.
It was a nightmare race for the three main championship contenders, as Fabio Quartararo and Bagnaia struggled for form while Aleix Espargaro was forced to change to his second Aprilia on the warm-up lap due to a mechanical issue.
A crash trying to pass Quartararo on the last lap led to a fifth DNF of the season for Bagnaia, gifting Quartararo an 18-point lead in the standings heading to next week’s Thailand GP.
Such was the limited amount of dry time the grid had this weekend at Motegi that numerous tyre changes took place ahead of lights out.
Poleman Marc Marquez went to the grid on a hard rear tyre, but switched to a soft for the start.
But he couldn’t use the early grip advantage that would have offered him to any effect. Though Marquez did convert his first pole in three years to the holeshot, he was muscled out by KTM’s Brad Binder at Turn 1.
Pramac Ducati rider Jorge Martin jumped up to second, before overtaking Binder for the lead into Turn 7 as Marquez was shuffled back to fifth.
Behind, the title challengers were all experiencing their struggles.
Drama struck at the end of the warm-up lap when Aprilia’s Espargaro pulled into pitlane for his second bike, dropping his broken first RS-GP as he made the switch.
Espargaro emerged from pitlane at the back of the pack behind the safety car, while Quartararo and Bagnaia failed to make up ground on the opening lap from their starting spots of ninth and 12th.
Miller’s charge from seventh on the grid saw him into the podium places began on the opening lap, with the factory Ducati rider passing Binder on the brakes into Turn 11 on the second tour.
The Australian, running the hard rear tyre, tried the same manoeuvre on Martin next time around.
Miller ran wide on the exit of Turn 11, allowing Martin to draw back alongside into the next left-hander at Turn 12 – though Miller held firm to end the third lap in the lead.
The factory Ducati rider repeatedly reeled off race-best laps as he quickly opened his lead out to over a second come lap nine of 24.
Martin would make an error a lap later which would give Miller a lead of over three seconds, which he would continue to extend out to over five seconds in the latter stages.
As drama struck behind him on the last lap for his Ducati teammate, Miller eased off to take the chequered flag…
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