| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Valentino Rossi | Movistar Yamaha | 323.4 | 01:59.947 | ||||
| 2 | Johann Zarco | Tech 3 | 320.9 | 02:00.024 | 0.077 / 0.077 | |||
| 3 | Dani Pedrosa | Repsol Honda | 320.6 | 02:00.087 | 0.140 / 0.063 | |||
| 4 | Andrea Dovizioso | Ducati | 323.6 | 02:00.124 | 0.177 / 0.037 | |||
| 5 | Jorge Lorenzo | Ducati | 319.5 | 02:00.149 | 0.202 / 0.025 | |||
| 6 | Jack Miller | EG 0,0 Marc VDS | 321.7 | 02:00.190 | 0.243 / 0.041 | |||
| 7 | Cal Crutchlow | LCR Honda | 320.3 | 02:00.199 | 0.252 / 0.009 | |||
| 8 | Andrea Iannone | Suzuki Ecstar | 321.8 | 02:00.394 | 0.447 / 0.195 | |||
| 9 | Marc Marquez | Repsol Honda | 321.5 | 02:00.467 | 0.520 / 0.073 | |||
| 10 | Maverick Viñales | Movistar Yamaha | 322.0 | 02:00.695 | 0.748 / 0.228 | |||
| 11 | Alex Rins | Suzuki Ecstar | 321.2 | 02:00.746 | 0.799 / 0.051 | |||
| 12 | Danilo Petrucci | Octo Pramac Racing | 324.6 | 02:00.864 | 0.917 / 0.118 | |||
| 13 | Karel Abraham | Pull&Bear Aspar | 323.5 | 02:00.876 | 0.929 / 0.012 | |||
| 14 | Bradley Smith | Red Bull KTM | 311.4 | 02:01.013 | 1.066 / 0.137 | |||
| 15 | Loris Baz | Reale Avintia Racing | 320.2 | 02:01.292 | 1.345 / 0.279 | |||
| 16 | Pol Espargaro | Red Bull KTM | 319.8 | 02:01.295 | 1.348 / 0.003 | |||
| 17 | Tito Rabat | EG 0,0 Marc VDS | 316.9 | 02:01.382 | 1.435 / 0.087 | |||
| 18 | Sam Lowes | Aprilia Gresini | 316.9 | 02:01.506 | 1.559 / 0.124 | |||
| 19 | Scott Redding | Octo Pramac Racing | 320.9 | 02:01.752 | 1.805 / 0.246 | |||
| 20 | Hector Barbera | Reale Avintia Racing | 316.7 | 02:01.847 | 1.900 / 0.095 | |||
| 21 | Michael van der Mark* | Tech 3 | 317.8 | 02:01.984 | 2.037 / 0.137 | |||
| 22 | Alvaro Bautista | Pull&Bear Aspar | 323.3 | 02:02.204 | 2.257 / 0.220 |
*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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