| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Marc Marquez | Repsol Honda | 322.5 | 02:00.438 | ||||
| 2 | Andrea Dovizioso | Ducati | 324.7 | 02:00.676 | 0.238 / 0.238 | |||
| 3 | Alex Rins | Suzuki Ecstar | 317.1 | 02:00.768 | 0.330 / 0.092 | |||
| 4 | Johann Zarco | Tech 3 | 316.6 | 02:00.870 | 0.432 / 0.102 | |||
| 5 | Dani Pedrosa | Repsol Honda | 318.2 | 02:00.873 | 0.435 / 0.003 | |||
| 6 | Jorge Lorenzo | Ducati | 322.1 | 02:00.875 | 0.437 / 0.002 | |||
| 7 | Jack Miller | EG 0,0 Marc VDS | 321.3 | 02:00.915 | 0.477 / 0.040 | |||
| 8 | Maverick Viñales | Movistar Yamaha | 321.9 | 02:01.042 | 0.604 / 0.127 | |||
| 9 | Valentino Rossi | Movistar Yamaha | 317.3 | 02:01.142 | 0.704 / 0.100 | |||
| 10 | Scott Redding | Octo Pramac Racing | 318.8 | 02:01.191 | 0.753 / 0.049 | |||
| 11 | Cal Crutchlow | LCR Honda | 320.4 | 02:01.224 | 0.786 / 0.033 | |||
| 12 | Karel Abraham | Pull&Bear Aspar | 320.7 | 02:01.228 | 0.790 / 0.004 | |||
| 13 | Andrea Iannone | Suzuki Ecstar | 320.9 | 02:01.233 | 0.795 / 0.005 | |||
| 14 | Alvaro Bautista | Pull&Bear Aspar | 323.3 | 02:01.235 | 0.797 / 0.002 | |||
| 15 | Danilo Petrucci | Octo Pramac Racing | 321.8 | 02:01.412 | 0.974 / 0.177 | |||
| 16 | Pol Espargaro | Red Bull KTM | 317.4 | 02:01.464 | 1.026 / 0.052 | |||
| 17 | Bradley Smith | Red Bull KTM | 309.8 | 02:01.768 | 1.330 / 0.304 | |||
| 18 | Hector Barbera | Reale Avintia Racing | 313.8 | 02:01.777 | 1.339 / 0.009 | |||
| 19 | Loris Baz | Reale Avintia Racing | 320.7 | 02:01.967 | 1.529 / 0.190 | |||
| 20 | Sam Lowes | Aprilia Gresini | 313.0 | 02:02.490 | 2.052 / 0.523 | |||
| 21 | Michael van der Mark* | Tech 3 | 316.2 | 02:02.697 | 2.259 / 0.207 | |||
| 22 | Tito Rabat | EG 0,0 Marc VDS | 317.6 | 02:03.000 | 2.562 / 0.303 |
*Replaced Jonas Folger for the Malaysian Grand Prix
Note: Aprilia Racing Team Gresini rider Aleix Espargaro did not take part in the Malaysian Grand Prix due to a hand injury he suffered at the Australian Grand Prix