Calificación Moto3 - Gran Premio de Japón 2016
| Pos. | Piloto | Equipo | Moto | Tiempo |
|---|---|---|---|---|
| 1 | 
Hiroki Ono |
Honda Team Asia | Honda | 1:56.443 |
| 2 | 
Andrea Migno |
SKY Racing Team VR46 | KTM | +0.086 |
| 3 | 
Brad Binder |
Red Bull KTM Ajo | KTM | +0.216 |
| 4 |
Enea Bastianini |
Gresini Racing Moto3 | Honda | +0.221 |
| 5 |
Nicolo Bulega |
SKY Racing Team VR46 | KTM | +0.230 |
| 6 |
Lorenzo Dalla Porta |
SKY Racing Team VR46 | KTM | +0.239 |
| 7 |
Niccolo Antonelli |
Ongetta-Rivacold | Honda | +0.297 |
| 8 | 
Fabio Quartararo |
Leopard Racing | KTM | +0.393 |
| 9 | 
Adam Norrodin |
Drive M7 SIC Racing Team | Honda | +0.430 |
| 10 | 
Philipp Oettl |
Schedl GP Racing | KTM | +0.456 |
| 11 | 
Jorge Navarro |
Estrella Galicia 0,0 | Honda | +0.508 |
| 12 |
Francesco Bagnaia |
ASPAR Mahindra Team Moto3 | Mahindra | +0.558 |
| 13 |
Albert Arenas |
Peugeot MC Saxo | Albert Arenas | +0.618 |
| 14 |
Joan Mir |
Leopard Racing | KTM | +0.619 |
| 15 | 
Livio Loi |
RW Racing GP BV | Honda | +0.639 |
| 16 | 
John Mcphee |
SaxoPrint RTG | Peugeot | +0.644 |
| 17 |
Arón Canet |
Estrella Galicia 0,0 | Honda | +0.710 |
| 18 |
Fabio Di Giannantonio |
Gresini Racing Moto3 | Honda | +0.744 |
| 19 | 
Gabriel Rodrigo |
RBA Racing Team | KTM | +0.777 |
| 20 |
Juanfran Guevara |
RBA Racing Team | KTM | +0.781 |
| 21 | 
Jakub Kornfeil |
Drive M7 SIC Racing Team | Honda | +0.793 |
| 22 |
Khairul Idham Pawi |
Honda Team Asia | Honda | +0.952 |
| 23 |
Adrián Martín |
MAPFRE Team MAHINDRA | Mahindra | +0.954 |
| 24 |
Jules Danilo |
Ongetta-Rivacold | Honda | +1.066 |
| 25 |
Tatsuki Suzuki |
CIP | Mahindra | +1.109 |
| 26 |
Marcos Ramírez |
Platinum Bay Real Estate | Mahindra | +1.238 |
| 27 | 
Bo Bendsneyder |
Red Bull KTM Ajo | KTM | +1.279 |
| 28 |
Darryn Binder |
Platinum Bay Real Estate | Mahindra | +1.401 |
| 29 |
Andrea Locatelli |
Leopard Racing | KTM | +2.063 |
| 30 |
María Herrera |
Team Laglisse | Honda | +2.800 |
| 31 |
Lorenzo Petrarca |
3570 Team Italia | Stefano Valtulini | +2.926 |
| 32 |
Fabio Spiranelli |
CIP | Mahindra | +2.937 |
| 33 |
Stefano Valtulini |
3570 Team Italia | Stefano Valtulini | +3.638 |
| 34 |
Shizuka Okazaki |
UQ & Teluru Kohara RT | Honda | +6.310 |
| 35 |
Rei Sato |
41 Planning IodaRacing Japan | Honda | +7.062 |