Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 29 | Andrea Iannone | Ongetta Team | 42'23.716 | 20 | 25 | 1 |
| 2 | 60 | Julian Simon | Bancaja Aspar Team 125cc | 42'25.062 | 20 | 20 | 2 |
| 3 | 44 | Pol Espargaro | Derbi Racing Team | 42'28.755 | 20 | 16 | 8 |
| 4 | 17 | Stefan Bradl | Viessmann Kiefer Racing | 42'30.620 | 20 | 13 | 3 |
| 5 | 93 | Marc Marquez | Red Bull Ktm Motosport | 42'36.777 | 20 | 11 | 10 |
| 6 | 11 | Sandro Cortese | Ajo Interwetten | 42'38.557 | 20 | 10 | 9 |
| 7 | 6 | Joan Olivé | Derbi Racing Team | 42'40.136 | 20 | 9 | 11 |
| 8 | 94 | Jonas Folger | Ongetta Team | 42'40.199 | 20 | 8 | 14 |
| 9 | 77 | Dominique Aegerter | Ajo Interwetten | 42'51.216 | 20 | 7 | 6 |
| 10 | 38 | Bradley Smith | Bancaja Aspar Team 125cc | 42'54.075 | 20 | 6 | 7 |
| 11 | 99 | Danny Webb | Degraaf Grand Prix | 43'01.263 | 20 | 5 | 13 |
| 12 | 71 | Tomoyoshi Koyama | Loncin Racing | 43'07.572 | 20 | 4 | 19 |
| 13 | 12 | Esteve Rabat | Blusens Aprilia | 43'23.605 | 20 | 3 | 4 |
| 14 | 8 | Lorenzo Zanetti | Ongetta Team | 43'23.857 | 20 | 2 | 15 |
| 15 | 24 | Simone Corsi | Jack & Jones Team | 43'26.317 | 20 | 1 | 17 |
| 16 | 16 | Cameron Beaubier | Red Bull Ktm Motosport | 43'26.325 | 20 | 0 | 23 |
| 17 | 18 | Nicolas Terol | Jack & Jones Team | 43'33.583 | 20 | 0 | 5 |
| 18 | 35 | Randy Krummenacher | Degraaf Grand Prix | 43'33.599 | 20 | 0 | 22 |
| 19 | 33 | Sergio Gadea | Bancaja Aspar Team 125cc | 43'38.765 | 20 | 0 | 12 |
| 20 | 73 | Takaaki Nakagami | Ongetta Team | 43'43.574 | 20 | 0 | 21 |
| 21 | 5 | Alexis Masbou | Loncin Racing | 44'07.129 | 20 | 0 | 25 |
| 22 | 7 | Efren Vazquez | Derbi Racing Team | 44'16.626 | 20 | 0 | 20 |
| 23 | 69 | Lukas Sembera | Matteoni Racing | 44'30.840 | 20 | 0 | 32 |
| 24 | 58 | Yuuchi Yanagisawa | 18 Garage Racing | 44'31.118 | 20 | 0 | 26 |
| 25 | 87 | Luca Marconi | CBC Corse | 42'36.873 | 19 | 0 | 30 |
| 26 | 10 | Luca Vitali | CBC Corse | 42'36.927 | 19 | 0 | 34 |
| 27 | 55 | Hiroomi Iwata | DYDO Miu Racing | 42'51.571 | 19 | 0 | 29 |
| 28 | 59 | Satoru Kamada | Endurance & Osl | 44'14.382 | 19 | 0 | 28 |
| 29 | 57 | Yuki Oogane | Endurance & Okegawajuku | 43'23.194 | 18 | 0 | 33 |
| 30 | 56 | Yuma Yahagi | Okegawajuku & Endurance | 25'49.120 | 11 | 0 | 27 |
| 31 | 14 | Johann Zarco | WTR San Marino Team | 22'27.306 | 10 | 0 | 18 |
| 32 | 45 | Scott Redding | Blusens Aprilia | 13'40.407 | 6 | 0 | 16 |
| 33 | 32 | Lorenzo Savadori | Fontana Racing | 4'37.688 | 2 | 0 | 24 |
| 34 | 53 | Jasper Iwema | Racing Team Germany | 0 | 0 | 31 |