Andrea Iannone took a hard-fought third win of the season at Motegi, as Marc Marquez finally captured the championship lead courtesy of finishing second.
From the outside of the front row Iannone (Speed Master Suter) passed Marquez (Catalunya Suter) on the run down to the first corner, the first move in a race-long battle between the pair.
Simone Corsi (Ioda FTR) and a charging Stefan Bradl, who had started eighth on the Kiefer Kalex, also got themselves involved, with the top four all covered by less than 1s.
On lap 7 Marquez found his way by Iannone on the pit straight, but that only spurred on the 22-year-old. He retook the lead several corners later and then set a series of fastest laps, with only Marquez able to stick with him.
Bradl meanwhile had worked his way past Corsi and looked like he may do enough to preserve a narrow championship advantage, until Thomas Luthi (Interwetten Suter) and Alex de Angelis (JIR Motobi) made it a four-way fight for third.
Bradl's aggressive start was taking its toll, and he was picked off by Luthi and then Corsi, dropping him to fifth. He fought back on the last lap to snatch fourth from Corsi, but even so knew he would lose a championship lead held since the very first race.
The damage was nearly made worse as Iannone seemed to find neutral and surrendered a 1s gap to Marquez, but the Italian attacked instantly and passed Marquez again to take his third win of the year.
Marquez now leads Bradl by one point as a result, with three races remaining.
De Angelis came home sixth, ahead of Bradley Smith (Tech 3), Dominique Aegerter (Technomag-CIP Suter) and Esteve Rabat (Blusens FTR).
Home favourite Yuki Takahashi crashed from a fight for 12th on lap 6, while the Pons Kalex squad saw Aleix Espargaro struggle and pit with tyre issues and Axel Pons retire in the gravel six laps from the finish.
Results - 23 laps:
Pos Rider Team/Bike Time/Gap 1. Andrea Iannone Speed Master Suter 43m25.007s 2. Marc Marquez Catalunya Suter + 1.999s 3. Thomas Luthi Interwetten Suter + 3.686s 4. Stefan Bradl Kiefer Kalex + 4.313s 5. Simone Corsi Ioda FTR + 4.647s 6. Alex de Angelis JIR Motobi + 4.813s 7. Bradley Smith Tech 3 + 10.520s 8. Dominique Aegerter Technomag-CIP Suter + 10.725s 9. Esteve Rabat Blusens FTR + 11.387s 10. Mika Kallio Marc VDS Suter + 12.803s 11. Xavier Simeon Tech 3 + 18.259s 12. Anthony West MZ + 20.815s 13. Michele Pirro Gresini Moriwaki + 23.795s 14. Mattia Pasini Ioda FTR + 24.388s 15. Pol Espargaro Speed Up FTR + 34.071s 16. Jules Cluzel Forward Suter + 38.236s 17. Kenny Noyes Avintia FTR + 39.505s 18. Max Neukirchner MZ + 39.609s 19. Kenan Sofuoglu Technomag-CIP Suter + 42.296s 20. Scott Redding Marc VDS Suter + 44.162s 21. Valentin Debise Speed Up FTR + 46.662s 22. Ratthapark Wilairot SAG FTR + 46.950s 23. Yonny Hernandez Blusens FTR + 49.625s 24. Randy Krummenacher Kiefer Kalex + 50.590s 25. Robertino Pietri Italtrans Suter + 52.044s 26. Joan Olive Castello FTR + 52.365s 27. Mike di Meglio Tech 3 + 1m02.873s 28. Tomoyoshi Koyama Technomag-CIP Suter + 1m35.559s 29. Mashel Al Naimi QMMF Moriwaki + 1m35.771s 30. Yuki Takahashi Gresini Moriwaki + 1 lap 31. Aleix Espargaro Pons Kalex + 3 laps Retirements: Axel Pons Pons Kalex 6 laps Santiago Hernandez SAG FTR 6 laps Jordi Torres Aspar Suter 0 laps Raffaele de Rosa Forward Suter 0 laps Ricard Cardus QMMF Moriwaki 0 laps