| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Joan Mir | Suzuki Ecstar | 326.2 | 01:59.516 | ||||
| 2 | Maverick Viñales | Monster Energy Yamaha | 323.3 | 01:59.784 | 0.268 / 0.268 | |||
| 3 | Franco Morbidelli | Petronas Yamaha | 320.4 | 01:59.832 | 0.316 / 0.048 | |||
| 4 | Marc Marquez | Repsol Honda | 327.2 | 01:59.857 | 0.341 / 0.025 | |||
| 5 | Andrea Dovizioso | Ducati | 332.3 | 01:59.913 | 0.397 / 0.056 | |||
| 6 | Fabio Quartararo | Petronas Yamaha | 322.3 | 01:59.916 | 0.400 / 0.003 | |||
| 7 | Valentino Rossi | Monster Energy Yamaha | 322.3 | 02:00.013 | 0.497 / 0.097 | |||
| 8 | Jack Miller | Pramac Racing | 331.2 | 02:00.023 | 0.507 / 0.010 | |||
| 9 | Pol Espargaro | Red Bull KTM | 320.4 | 02:00.172 | 0.656 / 0.149 | |||
| 10 | Cal Crutchlow | LCR Honda Castrol | 325.3 | 02:00.174 | 0.658 / 0.002 | |||
| 11 | Alex Rins | Suzuki Ecstar | 324.3 | 02:00.249 | 0.733 / 0.075 | |||
| 12 | Francesco Bagnaia | Pramac Racing | 327.2 | 02:00.339 | 0.823 / 0.090 | |||
| 13 | Aleix Espargaro | Aprilia Gresini | 324.3 | 02:00.359 | 0.843 / 0.020 | |||
| 14 | Danilo Petrucci | Ducati | 326.2 | 02:00.460 | 0.944 / 0.101 | |||
| 15 | Andrea Iannone | Aprilia Gresini | 323.3 | 02:00.525 | 1.009 / 0.065 | |||
| 16 | Johann Zarco* | LCR Honda Idemitsu | 323.3 | 02:00.667 | 1.151 / 0.142 | |||
| 17 | Karel Abraham | Reale Avintia Racing | 326.2 | 02:01.124 | 1.608 / 0.457 | |||
| 18 | Mika Kallio | Red Bull KTM | 319.5 | 02:01.238 | 1.722 / 0.114 | |||
| 19 | Jorge Lorenzo | Repsol Honda | 324.3 | 02:01.504 | 1.988 / 0.266 | |||
| 20 | Hafizh Syahrin | KTM Tech 3 | 320.4 | 02:02.224 | 2.708 / 0.720 |
*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