| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Franco Morbidelli | Petronas Yamaha | 323.3 | 01:59.600 | ||||
| 2 | Valentino Rossi | Monster Energy Yamaha | 320.4 | 01:59.796 | 0.196 / 0.196 | |||
| 3 | Andrea Dovizioso | Ducati | 330.2 | 01:59.957 | 0.357 / 0.161 | |||
| 4 | Fabio Quartararo | Petronas Yamaha | 322.3 | 01:59.973 | 0.373 / 0.016 | |||
| 5 | Marc Marquez | Repsol Honda | 328.2 | 01:59.980 | 0.380 / 0.007 | |||
| 6 | Maverick Viñales | Monster Energy Yamaha | 322.3 | 01:59.997 | 0.397 / 0.017 | |||
| 7 | Joan Mir | Suzuki Ecstar | 325.3 | 02:00.297 | 0.697 / 0.300 | |||
| 8 | Danilo Petrucci | Ducati | 324.3 | 02:00.326 | 0.726 / 0.029 | |||
| 9 | Jack Miller | Pramac Racing | 328.2 | 02:00.417 | 0.817 / 0.091 | |||
| 10 | Francesco Bagnaia | Pramac Racing | 330.2 | 02:00.538 | 0.938 / 0.121 | |||
| 11 | Alex Rins | Suzuki Ecstar | 325.3 | 02:00.642 | 1.042 / 0.104 | |||
| 12 | Pol Espargaro | Red Bull KTM | 322.3 | 02:00.744 | 1.144 / 0.102 | |||
| 13 | Andrea Iannone | Aprilia Gresini | 320.4 | 02:01.114 | 1.514 / 0.370 | |||
| 14 | Aleix Espargaro | Aprilia Gresini | 323.3 | 02:01.117 | 1.517 / 0.003 | |||
| 15 | Cal Crutchlow | LCR Honda Castrol | 324.3 | 02:01.159 | 1.559 / 0.042 | |||
| 16 | Johann Zarco* | LCR Honda Idemitsu | 323.3 | 02:01.342 | 1.742 / 0.183 | |||
| 17 | Jorge Lorenzo | Repsol Honda | 326.2 | 02:01.369 | 1.769 / 0.027 | |||
| 18 | Karel Abraham | Reale Avintia Racing | 325.3 | 02:01.474 | 1.874 / 0.105 | |||
| 19 | Hafizh Syahrin | KTM Tech 3 | 317.6 | 02:02.508 | 2.908 / 1.034 | |||
| 20 | Mika Kallio | Red Bull KTM | no time |
*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