| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Maverick Viñales | Movistar Yamaha | 325.2 | 01:59.231 | ||||
| 2 | Marc Marquez | Repsol Honda | 325.4 | 01:59.257 | 0.026 / 0.026 | |||
| 3 | Jack Miller | Alma Pramac Racing | 325.4 | 01:59.375 | 0.144 / 0.118 | |||
| 4 | Dani Pedrosa | Repsol Honda | 325.3 | 01:59.599 | 0.368 / 0.224 | |||
| 5 | Johann Zarco | Tech 3 | 321.5 | 01:59.655 | 0.424 / 0.056 | |||
| 6 | Danilo Petrucci | Alma Pramac Racing | 328.6 | 01:59.671 | 0.440 / 0.016 | |||
| 7 | Valentino Rossi | Movistar Yamaha | 323.8 | 01:59.773 | 0.542 / 0.102 | |||
| 8 | Andrea Iannone | Suzuki Ecstar | 325.4 | 01:59.799 | 0.568 / 0.026 | |||
| 9 | Alvaro Bautista | Angel Nieto Team | 326.3 | 02:00.130 | 0.899 / 0.331 | |||
| 10 | Franco Morbidelli | EG 0,0 Marc VDS | 321.0 | 02:00.405 | 1.174 / 0.275 | |||
| 11 | Stefan Bradl* | LCR Honda Castrol | 325.5 | 02:00.428 | 1.197 / 0.023 | |||
| 12 | Pol Espargaro | Red Bull KTM | 320.9 | 02:00.513 | 1.282 / 0.085 | |||
| 13 | Hafizh Syahrin | Tech 3 | 319.6 | 02:00.558 | 1.327 / 0.045 | |||
| 14 | Takaaki Nakagami | LCR Honda Idemitsu | 319.0 | 02:00.638 | 1.407 / 0.080 | |||
| 15 | Alex Rins | Suzuki Ecstar | 324.8 | 02:00.649 | 1.418 / 0.011 | |||
| 16 | Aleix Espargaro | Aprilia Gresini | 323.0 | 02:00.737 | 1.506 / 0.088 | |||
| 17 | Andrea Dovizioso | Ducati | 325.9 | 02:00.810 | 1.579 / 0.073 | |||
| 18 | Michele Pirro° | Ducati | 319.0 | 02:01.090 | 1.859 / 0.280 | |||
| 19 | Bradley Smith | Red Bull KTM | 318.4 | 02:01.223 | 1.992 / 0.133 | |||
| 20 | Karel Abraham | Angel Nieto Team | 318.2 | 02:01.385 | 2.154 / 0.162 | |||
| 21 | Thomas Luthi | EG 0,0 Marc VDS | 318.0 | 02:01.470 | 2.239 / 0.085 | |||
| 22 | Scott Redding | Aprilia Gresini | 318.9 | 02:02.442 | 3.211 / 0.972 | |||
| 23 | Jordi Torres^ | Reale Avintia Racing | 323.6 | 02:03.142 | 3.911 / 0.700 | |||
| 24 | Xavier Simeon | Reale Avintia Racing | 316.2 | 02:03.455 | 4.224 / 0.313 |
*Replaced Cal Crutchlow for the Malaysian Grand Prix
°Replaced Jorge Lorenzo from FP3 onwards
^Replaced Tito Rabat for the Malaysian Grand Prix
Note: Ducati Team's Jorge Lorenzo withdrew from the Malaysian Grand Prix following FP2 due to continued pain from his left wrist injury he sustained at the Thai Grand Prix