Carrera Moto3 Gran Premio de Malasia 2016
| Pos. | Piloto | Equipo | Moto | Tiempo |
|---|---|---|---|---|
| 1 | 
Francesco Bagnaia |
ASPAR Mahindra Team Moto3 | Mahindra | 29:29.351 |
| 2 | 
Jakub Kornfeil |
Drive M7 SIC Racing Team | Honda | +7.108 |
| 3 | 
Bo Bendsneyder |
Red Bull KTM Ajo | KTM | +7.253 |
| 4 | 
Fabio Quartararo |
Leopard Racing | KTM | +8.469 |
| 5 |
Andrea Locatelli |
Leopard Racing | KTM | +12.414 |
| 6 | 
Marcos Ramírez |
Platinum Bay Real Estate | Mahindra | +12.706 |
| 7 | 
Gabriel Rodrigo |
RBA Racing Team | KTM | +13.387 |
| 8 | 
Khairul Idham Pawi |
Honda Team Asia | Honda | +13.506 |
| 9 | 
Livio Loi |
RW Racing GP BV | Honda | +14.445 |
| 10 | 
Darryn Binder |
Platinum Bay Real Estate | Mahindra | +38.777 |
| 11 |
Hafiq Azmi |
Peugeot MC Saxoprint | Peugeot | +45.827 |
| 12 |
Niccolo Antonelli |
Ongetta-Rivacold | Honda | +48.899 |
| 13 |
Stefano Valtulini |
3570 Team Italia | Stefano Valtulini | +49.648 |
| 14 |
Lorenzo Petrarca |
3570 Team Italia | Stefano Valtulini | +49.842 |
| 15 |
Fabio Di Giannantonio |
Gresini Racing Moto3 | Honda | +1:15.163 |
| 16 |
Lorenzo Dalla Porta |
SKY Racing Team VR46 | KTM | 1 Vuelta |
| 17 |
Brad Binder |
Red Bull KTM Ajo | KTM | 3 Vueltas |
| 18 |
María Herrera |
Team Laglisse | Honda | +13.793 |
| 19 |
Jules Danilo |
Ongetta-Rivacold | Honda | 7 Vueltas |
| 20 |
Jorge Navarro |
Estrella Galicia 0,0 | Honda | 8 Vueltas |
| 21 |
Albert Arenas |
Peugeot MC Saxo | Albert Arenas | 10 Vueltas |
| 22 |
Joan Mir |
Leopard Racing | KTM | 11 Vueltas |
| 23 | 
Tatsuki Suzuki |
CIP | Mahindra | 11 Vueltas |
| 24 |
Andrea Migno |
SKY Racing Team VR46 | KTM | 11 Vueltas |
| 25 |
Nicolo Bulega |
SKY Racing Team VR46 | KTM | 12 Vueltas |
| 26 |
Adrián Martín |
MAPFRE Team MAHINDRA | Mahindra | 0 Vuelta |
| 27 |
Arón Canet |
Estrella Galicia 0,0 | Honda | 0 Vuelta |
| 28 | 
Philipp Oettl |
Schedl GP Racing | KTM | 0 Vuelta |
| 29 |
Juanfran Guevara |
RBA Racing Team | KTM | 0 Vuelta |
| 30 |
Adam Norrodin |
Drive M7 SIC Racing Team | Honda | 0 Vuelta |
| 31 | 
Alex Fabbri |
0 Vuelta |