| P | Rider | Team | Km/h | Time/Gap | ||||
|---|---|---|---|---|---|---|---|---|
| 1 | Marc Marquez | Repsol Honda | 162.2 | 42:36.438 | ||||
| 2 | Cal Crutchlow | LCR Honda Castrol | 162.1 | +1.573 | ||||
| 3 | Alex Rins | Suzuki Ecstar | 162.1 | +1.720 | ||||
| 4 | Valentino Rossi | Movistar Yamaha | 161.8 | +6.413 | ||||
| 5 | Alvaro Bautista | Angel Nieto Team | 161.8 | +6.919 | ||||
| 6 | Johann Zarco | Tech 3 | 161.7 | +8.024 | ||||
| 7 | Maverick Viñales | Movistar Yamaha | 161.4 | +13.330 | ||||
| 8 | Dani Pedrosa | Repsol Honda | 161.2 | +15.582 | ||||
| 9 | Danilo Petrucci | Alma Pramac Racing | 160.9 | +20.584 | ||||
| 10 | Hafizh Syahrin | Tech 3 | 160.6 | +24.985 | ||||
| 11 | Franco Morbidelli | EG 0,0 Marc VDS | 160.6 | +25.931 | ||||
| 12 | Bradley Smith | Red Bull KTM | 160.5 | +26.875 | ||||
| 13 | Pol Espargaro | Red Bull KTM | 160.5 | +27.069 | ||||
| 14 | Katsuyuki Nakasuga* | Yamalube Racing | 160.2 | +32.550 | ||||
| 15 | Takaaki Nakagami | LCR Honda Idemitsu | 159.9 | +37.718 | ||||
| 16 | Xavier Simeon | Reale Avintia Racing | 159.7 | +39.583 | ||||
| 17 | Jordi Torres^ | Reale Avintia Racing | 159.7 | +39.839 | ||||
| 18 | Andrea Dovizioso | Ducati | 159.5 | +42.698 | ||||
| 19 | Scott Redding | Aprilia Gresini | 159.1 | +49.943 | ||||
| 20 | Thomas Luthi | EG 0,0 Marc VDS | 158.9 | +52.707 | ||||
| 21 | Sylvain Guintoli* | Suzuki Ecstar | 158.4 | +1:01.848 | ||||
| Not Classified | ||||||||
| Andrea Iannone | Suzuki Ecstar | 161.7 | 10 Laps | |||||
| Karel Abraham | Angel Nieto Team | 152.6 | 12 Laps | |||||
| Jack Miller | Alma Pramac Racing | 161.0 | 14 Laps | |||||
| Aleix Espargaro | Aprilia Gresini | 157.1 | 18 Laps | |||||
*Wild card entry
^Replaced Tito Rabat for the Japanese Grand Prix
Note: Repsol Honda rider Marc Marquez claimed the 2018 MotoGP Riders' title in Motegi
Ducati Team's Jorge Lorenzo withdrew from the Japanese Grand Prix after completing two laps in FP1