| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Franco Morbidelli | Petronas Yamaha | 320.4 | 01:58.761 | ||||
| 2 | Fabio Quartararo | Petronas Yamaha | 320.4 | 01:58.977 | 0.216 / 0.216 | |||
| 3 | Marc Marquez | Repsol Honda | 326.2 | 01:59.066 | 0.305 / 0.089 | |||
| 4 | Maverick Viñales | Monster Energy Yamaha | 324.3 | 01:59.074 | 0.313 / 0.008 | |||
| 5 | Jack Miller | Pramac Racing | 329.2 | 01:59.227 | 0.466 / 0.153 | |||
| 6 | Francesco Bagnaia | Pramac Racing | 327.2 | 01:59.253 | 0.492 / 0.026 | |||
| 7 | Alex Rins | Suzuki Ecstar | 324.3 | 01:59.401 | 0.640 / 0.148 | |||
| 8 | Johann Zarco* | LCR Honda Idemitsu | 324.3 | 01:59.486 | 0.725 / 0.085 | |||
| 9 | Joan Mir | Suzuki Ecstar | 326.2 | 01:59.501 | 0.740 / 0.015 | |||
| 10 | Cal Crutchlow | LCR Honda Castrol | 324.3 | 01:59.535 | 0.774 / 0.034 | |||
| 11 | Aleix Espargaro | Aprilia Gresini | 321.4 | 01:59.564 | 0.803 / 0.029 | |||
| 12 | Valentino Rossi | Monster Energy Yamaha | 322.3 | 01:59.643 | 0.882 / 0.079 | |||
| 13 | Danilo Petrucci | Ducati | 328.2 | 01:59.754 | 0.993 / 0.111 | |||
| 14 | Andrea Dovizioso | Ducati | 331.2 | 02:00.244 | 1.483 / 0.490 | |||
| 15 | Karel Abraham | Reale Avintia Racing | 329.2 | 02:00.290 | 1.529 / 0.046 | |||
| 16 | Pol Espargaro | Red Bull KTM | 321.4 | 02:00.353 | 1.592 / 0.063 | |||
| 17 | Jorge Lorenzo | Repsol Honda | 323.3 | 02:00.406 | 1.645 / 0.053 | |||
| 18 | Andrea Iannone | Aprilia Gresini | 322.3 | 02:00.645 | 1.884 / 0.239 | |||
| 19 | Mika Kallio | Red Bull KTM | 319.5 | 02:00.988 | 2.227 / 0.343 | |||
| 20 | Hafizh Syahrin | KTM Tech 3 | 317.6 | 02:01.980 | 3.219 / 0.992 |
*Replaced Takaaki Nakagami for the Malaysian Grand Prix
Note: Red Bull KTM Tech 3 rider Miguel Oliveira withdrew from the Malaysian Grand Prix after completing four laps in FP1
Reale Avintia Racing rider Tito Rabat did not take part in the Malaysian Grand Prix due to a hand injury