Marc Marquez turned his first Motegi pole into his tenth win of 2019, heading Petronas SRT’s Fabio Quartararo at the end of the 25-lap encounter, for his 10th win of his title-winning campaign.
Marquez got a perfect launch to maintain his pole advantage into Turn 1 ahead of Quartararo and a similarly fast-starting Jack Miller.
Quartararo – keen to finally take his first premier class victory – dived past Marquez into Turn 7, but not to be denied the Honda was back through with a late move into the Turn 9 hairpin.
Marquez then was able to build an advantage of around 1.2 seconds over the next lap, before the chasing Frenchman began to slowly reel him back in.
The gap between the leading pair yo-yoed by a just a few tenths over the following 10 laps, before Marquez pulled the pin just after half-distance and doubled his advantage to well over two seconds over the subsequent tours.
The newly-crowned six-time MotoGP champion then controlled his lead across the remaining laps to take the chequered flag just under two seconds ahead of Quartararo, who held off a charging Andrea Dovizioso for his fourth runner-up result of the season.
The battle for third looked to be going the way of Maverick Vinales over the closing laps, with the Yamaha man pressuring Dovizioso hard while the pair closed on Quartararo.
The Italian was stoic in defence though, and ultimately secured third ahead of the factory M1 rider.
Franco Morbidelli was pipped to fifth by Cal Crutchlow on the run to the line after looking good for his maiden podium finish early on, having passed the struggling Miller for the position.
The Italian was unable to sustain the pace of Dovizioso and Vinales though and dropped back after being overthrown from third towards the chasing LCR Honda and Alex Rins’ Suzuki.
Crutchlow then got a brilliant exit from the final corner on the last lap to draft past the Yamaha shortly before the line, demoting Morbidelli to sixth just ahead of Rins.
Joan Mir was eighth on the second GSX-RR, while Danilo Petrucci got the best of the fading Miller for ninth in the last couple of laps.
Valentino Rossi suffered a horror race meanwhile, crashing out from a distant 11th with just five laps remaining, while the only other non-finisher was Esteve Rabat, who decided to not even start the race after he was handed a pit-lane start penalty for exceeding his engine allocation.