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.