| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Fabio Quartararo | Petronas Yamaha | 322.3 | 01:58.576 | ||||
| 2 | Andrea Dovizioso | Ducati | 329.2 | 01:59.206 | 0.630 / 0.630 | |||
| 3 | Valentino Rossi | Monster Energy Yamaha | 322.3 | 01:59.284 | 0.708 / 0.078 | |||
| 4 | Franco Morbidelli | Petronas Yamaha | 321.4 | 01:59.502 | 0.926 / 0.218 | |||
| 5 | Jack Miller | Pramac Racing | 328.2 | 01:59.593 | 1.017 / 0.091 | |||
| 6 | Aleix Espargaro | Aprilia Gresini | 326.2 | 01:59.707 | 1.131 / 0.114 | |||
| 7 | Cal Crutchlow | LCR Honda Castrol | 326.2 | 01:59.711 | 1.135 / 0.004 | |||
| 8 | Francesco Bagnaia | Pramac Racing | 322.3 | 01:59.774 | 1.198 / 0.063 | |||
| 9 | Maverick Viñales | Monster Energy Yamaha | 320.4 | 01:59.845 | 1.269 / 0.071 | |||
| 10 | Alex Rins | Suzuki Ecstar | 323.3 | 01:59.849 | 1.273 / 0.004 | |||
| 11 | Joan Mir | Suzuki Ecstar | 324.3 | 01:59.984 | 1.408 / 0.135 | |||
| 12 | Danilo Petrucci | Ducati | 327.2 | 02:00.057 | 1.481 / 0.073 | |||
| 13 | Marc Marquez | Repsol Honda | 324.3 | 02:00.215 | 1.639 / 0.158 | |||
| 14 | Johann Zarco* | LCR Honda Idemitsu | 325.3 | 02:00.268 | 1.692 / 0.053 | |||
| 15 | Karel Abraham | Reale Avintia Racing | 323.3 | 02:00.477 | 1.901 / 0.209 | |||
| 16 | Pol Espargaro | Red Bull KTM | 322.3 | 02:00.658 | 2.082 / 0.181 | |||
| 17 | Jorge Lorenzo | Repsol Honda | 324.3 | 02:00.705 | 2.129 / 0.047 | |||
| 18 | Andrea Iannone | Aprilia Gresini | 321.4 | 02:01.190 | 2.614 / 0.485 | |||
| 19 | Mika Kallio | Red Bull KTM | 319.5 | 02:02.017 | 3.441 / 0.827 | |||
| 20 | Hafizh Syahrin | KTM Tech 3 | 316.7 | 02:02.429 | 3.853 / 0.412 |
*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