Andrea Dovizioso remains the fastest man so far at Motegi after FP3, leading the charge to Q2 ahead of title rival Marc Marquez.
Aeix Espargaro remains third, just ahead of Ducati Team’s Jorge Lorenzo.
The biggest news saw Italian Valentino Rossi dig deep after a tough time for the Yamaha factory bikes in the wet on Friday, and the nine-time World Champion managed to get into the top ten and then the top five.
Teammate Maverick Viñales was the big name left out, and the Spaniard will head through Q1.
Johann Zarco goes through once more in P6, ahead of a positive weekend so far for Andrea Iannone in seventh. Danilo Petrucci, after a difficult Aragon, was back in the mix in eighth.
Dani Pedrosa went safely through in P9, with Alex Rins the final automatic entrant to Q2 after proving one of the 12 riders to improve his time on Saturday morning – making it both Hamamatsu factory machines moving through.
Q2 Result:
| Pos | Rider | Team | Km/h | Time | Gap 1st/Prev |
| 1 | Marc MARQUEZ | Repsol Honda Team | 298.3 | 1’55.254 | |
| 2 | Valentino ROSSI | Movistar Yamaha MotoGP | 295.1 | 1’55.283 | 0.029 / 0.029 |
| 3 | Andrea IANNONE | Team SUZUKI ECSTAR | 298 | 1’55.499 | 0.245 / 0.216 |
| 4 | Jorge LORENZO | Ducati Team | 294.9 | 1’55.558 | 0.304 / 0.059 |
| 5 | Aleix ESPARGARO | Aprilia Racing Team Gresini | 298.1 | 1’55.655 | 0.401 / 0.097 |
| 6 | Alex RINS | Team SUZUKI ECSTAR | 298.8 | 1’56.139 | 0.885 / 0.484 |
| 7 | Pol ESPARGARO | Red Bull KTM Factory Racing | 298.5 | 1’56.218 | 0.964 / 0.079 |
| 8 | Johann ZARCO | Monster Yamaha Tech 3 | 297.6 | 1’56.257 | 1.003 / 0.039 |
| 9 | Dani PEDROSA | Repsol Honda Team | 288.5 | 1’56.267 | 1.013 / 0.010 |
| 10 | Sam LOWES | Aprilia Racing Team Gresini | 293.2 | 1’56.281 | 1.027 / 0.014 |
| 11 | Danilo PETRUCCI | OCTO Pramac Racing | 299.4 | 1’56.329 | 1.075 / 0.048 |
| 12 | Maverick VIÑALES | Movistar Yamaha MotoGP | 297.2 | 1’56.354 | 1.100 / 0.025 |
| 13 | Andrea DOVIZIOSO | Ducati Team | 297.3 | 1’56.383 | 1.129 / 0.029 |
| 14 | Alvaro BAUTISTA | Pull&Bear Aspar Team | 295.2 | 1’56.498 | 1.244 / 0.115 |
| 15 | Cal CRUTCHLOW | LCR Honda | 291.4 | 1’56.787 | 1.533 / 0.289 |
| 16 | Bradley SMITH | Red Bull KTM Factory Racing | 291.4 | 1’56.840 | 1.586 / 0.053 |
| 17 | Hiroshi AOYAMA | EG 0,0 Marc VDS | 297.4 | 1’57.218 | 1.964 / 0.378 |
| 18 | Loris BAZ | Reale Avintia Racing | 292.1 | 1’57.237 | 1.983 / 0.019 |
| 19 | Tito RABAT | EG 0,0 Marc VDS | 292.2 | 1’57.247 | 1.993 / 0.010 |
| 20 | Karel ABRAHAM | Pull&Bear Aspar Team | 293.5 | 1’57.405 | 2.151 / 0.158 |
| 21 | Hector BARBERA | Reale Avintia Racing | 295.2 | 1’57.463 | 2.209 / 0.058 |
| 22 | Kohta NOZANE | Monster Yamaha Tech 3 | 295.8 | 1’57.497 | 2.243 / 0.034 |
| 23 | Katsuyuki NAKASUGA | Yamalube Yamaha Factory Racing | 293.7 | 1’58.528 | 3.274 / 1.031 |
| 24 | Scott REDDING | OCTO Pramac Racing | 293.6 | 1’58.730 | 3.476 / 0.202 |