| P | Rider | Team | Km/h | Time/Gap | ||||
|---|---|---|---|---|---|---|---|---|
| 1 | Marc Marquez | Repsol Honda | 164.0 | 40:32.372 | ||||
| 2 | Alex Rins | Suzuki Ecstar | 163.9 | +1.898 | ||||
| 3 | Johann Zarco | Tech 3 | 163.9 | +2.474 | ||||
| 4 | Maverick Viñales | Movistar Yamaha | 163.7 | +4.667 | ||||
| 5 | Dani Pedrosa | Repsol Honda | 163.6 | +6.190 | ||||
| 6 | Andrea Dovizioso | Ducati | 163.3 | +11.248 | ||||
| 7 | Alvaro Bautista | Angel Nieto Team | 163.0 | +15.611 | ||||
| 8 | Jack Miller | Alma Pramac Racing | 162.8 | +19.009 | ||||
| 9 | Danilo Petrucci | Alma Pramac Racing | 162.5 | +22.921 | ||||
| 10 | Hafizh Syahrin | Tech 3 | 162.2 | +26.919 | ||||
| 11 | Aleix Espargaro | Aprilia Gresini | 162.1 | +29.503 | ||||
| 12 | Franco Morbidelli | EG 0,0 Marc VDS | 162.0 | +30.933 | ||||
| 13 | Stefan Bradl* | LCR Honda Castrol | 161.7 | +35.322 | ||||
| 14 | Takaaki Nakagami | LCR Honda Idemitsu | 161.5 | +37.912 | ||||
| 15 | Bradley Smith | Red Bull KTM | 161.4 | +39.675 | ||||
| 16 | Thomas Luthi | EG 0,0 Marc VDS | 161.3 | +41.820 | ||||
| 17 | Xavier Simeon | Reale Avintia Racing | 161.1 | +43.978 | ||||
| 18 | Valentino Rossi | Movistar Yamaha | 160.2 | +58.288 | ||||
| 19 | Scott Redding | Aprilia Gresini | 160.1 | +1:00.191 | ||||
| Not Classified | ||||||||
| Pol Espargaro | Red Bull KTM | 162.1 | 4 Laps | |||||
| Michele Pirro° | Ducati | 160.8 | 15 Laps | |||||
| Karel Abraham | Angel Nieto Team | 157.9 | 17 Laps | |||||
| Andrea Iannone | Suzuki Ecstar | 20 Laps | ||||||
*Replaced Cal Crutchlow for the Malaysian Grand Prix
°Replaced Jorge Lorenzo from FP3 onwards
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