| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Andrea Dovizioso | Ducati | 326.8 | 02:00.456 | ||||
| 2 | Johann Zarco | Tech 3 | 322.2 | 02:00.466 | 0.010 / 0.010 | |||
| 3 | Valentino Rossi | Movistar Yamaha | 323.1 | 02:00.485 | 0.029 / 0.019 | |||
| 4 | Dani Pedrosa | Repsol Honda | 320.8 | 02:00.571 | 0.115 / 0.086 | |||
| 5 | Andrea Iannone | Suzuki Ecstar | 324.3 | 02:00.657 | 0.201 / 0.086 | |||
| 6 | Jorge Lorenzo | Ducati | 322.8 | 02:00.661 | 0.205 / 0.004 | |||
| 7 | Jack Miller | EG 0,0 Marc VDS | 322.9 | 02:00.713 | 0.257 / 0.052 | |||
| 8 | Marc Marquez | Repsol Honda | 323.0 | 02:00.729 | 0.273 / 0.016 | |||
| 9 | Karel Abraham | Pull&Bear Aspar | 321.1 | 02:00.766 | 0.310 / 0.037 | |||
| 10 | Maverick Viñales | Movistar Yamaha | 322.5 | 02:00.806 | 0.350 / 0.040 | |||
| 11 | Cal Crutchlow | LCR Honda | 318.3 | 02:00.823 | 0.367 / 0.017 | |||
| 12 | Alex Rins | Suzuki Ecstar | 321.7 | 02:00.827 | 0.371 / 0.004 | |||
| 13 | Hector Barbera | Reale Avintia Racing | 319.1 | 02:01.133 | 0.677 / 0.306 | |||
| 14 | Scott Redding | Octo Pramac Racing | 321.5 | 02:01.157 | 0.701 / 0.024 | |||
| 15 | Alvaro Bautista | Pull&Bear Aspar | 327.7 | 02:01.341 | 0.885 / 0.184 | |||
| 16 | Bradley Smith | Red Bull KTM | 310.5 | 02:01.399 | 0.943 / 0.058 | |||
| 17 | Danilo Petrucci | Octo Pramac Racing | 324.2 | 02:01.400 | 0.944 / 0.001 | |||
| 18 | Tito Rabat | EG 0,0 Marc VDS | 318.3 | 02:01.466 | 1.010 / 0.066 | |||
| 19 | Loris Baz | Reale Avintia Racing | 322.0 | 02:01.602 | 1.146 / 0.136 | |||
| 20 | Pol Espargaro | Red Bull KTM | 321.5 | 02:01.663 | 1.207 / 0.061 | |||
| 21 | Sam Lowes | Aprilia Gresini | 315.1 | 02:01.776 | 1.320 / 0.113 | |||
| 22 | Michael van der Mark* | Tech 3 | 317.3 | 02:02.222 | 1.766 / 0.446 |
*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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