| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Andrea Dovizioso | Ducati | 305.6 | 02:11.640 | ||||
| 2 | Marc Marquez | Repsol Honda | 307.6 | 02:12.166 | 0.526 / 0.526 | |||
| 3 | Jorge Lorenzo | Ducati | 303.4 | 02:12.695 | 1.055 / 0.529 | |||
| 4 | Maverick Viñales | Movistar Yamaha | 302.0 | 02:12.878 | 1.238 / 0.183 | |||
| 5 | Danilo Petrucci | Octo Pramac Racing | 303.7 | 02:13.048 | 1.408 / 0.170 | |||
| 6 | Valentino Rossi | Movistar Yamaha | 297.9 | 02:13.071 | 1.431 / 0.023 | |||
| 7 | Alvaro Bautista | Pull&Bear Aspar | 303.5 | 02:13.291 | 1.651 / 0.220 | |||
| 8 | Alex Rins | Suzuki Ecstar | 305.3 | 02:13.416 | 1.776 / 0.125 | |||
| 9 | Andrea Iannone | Suzuki Ecstar | 293.0 | 02:13.483 | 1.843 / 0.067 | |||
| 10 | Sam Lowes | Aprilia Gresini | 296.2 | 02:13.561 | 1.921 / 0.078 | |||
| 11 | Johann Zarco | Tech 3 | 308.3 | 02:13.648 | 2.008 / 0.087 | |||
| 12 | Jack Miller | EG 0,0 Marc VDS | 305.6 | 02:13.740 | 2.100 / 0.092 | |||
| 13 | Karel Abraham | Pull&Bear Aspar | 291.3 | 02:13.760 | 2.120 / 0.020 | |||
| 14 | Cal Crutchlow | LCR Honda | 291.6 | 02:13.872 | 2.232 / 0.112 | |||
| 15 | Scott Redding | Octo Pramac Racing | 292.6 | 02:14.281 | 2.641 / 0.409 | |||
| 16 | Pol Espargaro | Red Bull KTM | 295.1 | 02:14.287 | 2.647 / 0.006 | |||
| 17 | Bradley Smith | Red Bull KTM | 293.9 | 02:14.543 | 2.903 / 0.256 | |||
| 18 | Dani Pedrosa | Repsol Honda | 290.0 | 02:14.574 | 2.934 / 0.031 | |||
| 19 | Michael van der Mark* | Tech 3 | 306.1 | 02:14.938 | 3.298 / 0.364 | |||
| 20 | Hector Barbera | Reale Avintia Racing | 284.0 | 02:15.163 | 3.523 / 0.225 | |||
| 21 | Tito Rabat | EG 0,0 Marc VDS | 301.6 | 02:16.280 | 4.640 / 1.117 | |||
| 22 | Loris Baz | Reale Avintia Racing | 303.1 | 02:17.627 | 5.987 / 1.347 |
*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