| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Andrea Dovizioso | Ducati | 326.0 | 02:00.671 | ||||
| 2 | Alvaro Bautista | Pull&Bear Aspar | 326.2 | 02:00.742 | 0.071 / 0.071 | |||
| 3 | Johann Zarco | Tech 3 | 320.8 | 02:00.807 | 0.136 / 0.065 | |||
| 4 | Maverick Viñales | Movistar Yamaha | 321.0 | 02:00.903 | 0.232 / 0.096 | |||
| 5 | Marc Marquez | Repsol Honda | 322.0 | 02:00.950 | 0.279 / 0.047 | |||
| 6 | Cal Crutchlow | LCR Honda | 310.6 | 02:01.060 | 0.389 / 0.110 | |||
| 7 | Karel Abraham | Pull&Bear Aspar | 315.8 | 02:01.077 | 0.406 / 0.017 | |||
| 8 | Hector Barbera | Reale Avintia Racing | 313.4 | 02:01.147 | 0.476 / 0.070 | |||
| 9 | Dani Pedrosa | Repsol Honda | 318.1 | 02:01.162 | 0.491 / 0.015 | |||
| 10 | Jorge Lorenzo | Ducati | 318.7 | 02:01.189 | 0.518 / 0.027 | |||
| 11 | Danilo Petrucci | Octo Pramac Racing | 328.4 | 02:01.560 | 0.889 / 0.371 | |||
| 12 | Valentino Rossi | Movistar Yamaha | 318.1 | 02:01.662 | 0.991 / 0.102 | |||
| 13 | Andrea Iannone | Suzuki Ecstar | 317.9 | 02:01.740 | 1.069 / 0.078 | |||
| 14 | Jack Miller | EG 0,0 Marc VDS | 320.2 | 02:01.803 | 1.132 / 0.063 | |||
| 15 | Pol Espargaro | Red Bull KTM | 317.5 | 02:01.831 | 1.160 / 0.028 | |||
| 16 | Loris Baz | Reale Avintia Racing | 315.4 | 02:02.416 | 1.745 / 0.585 | |||
| 17 | Bradley Smith | Red Bull KTM | 308.5 | 02:02.469 | 1.798 / 0.053 | |||
| 18 | Scott Redding | Octo Pramac Racing | 317.9 | 02:03.056 | 2.385 / 0.587 | |||
| 19 | Michael van der Mark* | Tech 3 | 314.6 | 02:03.473 | 2.802 / 0.417 | |||
| 20 | Tito Rabat | EG 0,0 Marc VDS | 305.1 | 02:03.531 | 2.860 / 0.058 | |||
| 21 | Sam Lowes | Aprilia Gresini | 309.2 | 02:03.534 | 2.863 / 0.003 | |||
| 22 | Alex Rins | Suzuki Ecstar | 313.2 | 02:04.381 | 3.710 / 0.847 |
*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
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