| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Maverick Viñales | Movistar Yamaha | 299.8 | 02:11.476 | ||||
| 2 | Valentino Rossi | Movistar Yamaha | 297.2 | 02:12.424 | 0.948 / 0.948 | |||
| 3 | Jack Miller | Alma Pramac Racing | 301.5 | 02:12.903 | 1.427 / 0.479 | |||
| 4 | Marc Marquez | Repsol Honda | 308.8 | 02:13.007 | 1.531 / 0.104 | |||
| 5 | Michele Pirro° | Ducati | 294.3 | 02:13.530 | 2.054 / 0.523 | |||
| 6 | Scott Redding | Aprilia Gresini | 301.8 | 02:13.631 | 2.155 / 0.101 | |||
| 7 | Andrea Dovizioso | Ducati | 294.3 | 02:13.788 | 2.312 / 0.157 | |||
| 8 | Alex Rins | Suzuki Ecstar | 308.7 | 02:13.847 | 2.371 / 0.059 | |||
| 9 | Alvaro Bautista | Angel Nieto Team | 303.8 | 02:13.934 | 2.458 / 0.087 | |||
| 10 | Dani Pedrosa | Repsol Honda | 294.2 | 02:14.305 | 2.829 / 0.371 | |||
| 11 | Karel Abraham | Angel Nieto Team | 286.0 | 02:14.458 | 2.982 / 0.153 | |||
| 12 | Pol Espargaro | Red Bull KTM | 294.1 | 02:14.496 | 3.020 / 0.038 | |||
| 13 | Danilo Petrucci | Alma Pramac Racing | 299.0 | 02:14.587 | 3.111 / 0.091 | |||
| 14 | Johann Zarco | Tech 3 | 292.6 | 02:14.625 | 3.149 / 0.038 | |||
| 15 | Hafizh Syahrin | Tech 3 | 295.8 | 02:14.940 | 3.464 / 0.315 | |||
| 16 | Xavier Simeon | Reale Avintia Racing | 285.8 | 02:14.978 | 3.502 / 0.038 | |||
| 17 | Stefan Bradl* | LCR Honda Castrol | 285.7 | 02:15.743 | 4.267 / 0.765 | |||
| 18 | Aleix Espargaro | Aprilia Gresini | 301.2 | 02:15.932 | 4.456 / 0.189 | |||
| 19 | Bradley Smith | Red Bull KTM | 273.2 | 02:15.952 | 4.476 / 0.020 | |||
| 20 | Franco Morbidelli | EG 0,0 Marc VDS | 295.0 | 02:16.048 | 4.572 / 0.096 | |||
| 21 | Thomas Luthi | EG 0,0 Marc VDS | 286.3 | 02:16.141 | 4.665 / 0.093 | |||
| 22 | Takaaki Nakagami | LCR Honda Idemitsu | 287.6 | 02:16.218 | 4.742 / 0.077 | |||
| 23 | Andrea Iannone | Suzuki Ecstar | 281.0 | 02:20.917 | 9.441 / 4.699 |
°Replaced Jorge Lorenzo from FP3 onwards
*Replaced Cal Crutchlow 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
Reale Avintia Racing rider Jordi Torres was declared unfit for the Malaysian Grand Prix after suffering a hand injury during FP4