Calificación MotoGP - Gran Premio de Japón 2013
| Pos. | Piloto | Equipo | Moto | Tiempo |
|---|---|---|---|---|
| 1 | 
Jorge Lorenzo |
Yamaha Factory Racing | Yamaha | 1:53.471 |
| 2 |
Marc Márquez |
Repsol Honda Team | Honda | +0.658 |
| 3 | 
Nicky Hayden |
Ducati Team | Ducati | +1.068 |
| 4 |
Dani Pedrosa |
Repsol Honda Team | Honda | +1.071 |
| 5 | 
Valentino Rossi |
Yamaha Factory Racing | Yamaha | +1.261 |
| 6 |
Andrea Dovizioso |
Ducati Team | Ducati | +1.565 |
| 7 |
Alvaro Bautista |
GO&FUN Honda Gresini | Honda | +1.664 |
| 8 | 
Stefan Bradl |
LCR Honda MotoGP | Honda | +2.139 |
| 9 |
Aleix Espargaró |
Power Electronics Aspar | Aprilia | +2.248 |
| 10 | 
Yonny Hernandez |
Paul Bird Motorsport | ART-Aprilia | +2.527 |
| 11 | 
Cal Crutchlow |
Monster Yamaha Tech 3 | Yamaha | +2.587 |
| 12 | 
Katsuyuki Nakasuga |
Yamaha YSP Racing Team | Yamaha | +2.654 |
| 13 | 
Bradley Smith |
Monster Yamaha Tech 3 | Yamaha | +3.643 |
| 14 |
Colin Edwards |
NGM Mobile Forward Racing | Suter | +3.826 |
| 15 |
Andrea Iannone |
Pramac Racing Team | Ducati | +3.876 |
| 16 |
Danilo Petrucci |
Came IodaRacing Project | FTR | +4.069 |
| 17 | 
Randy De Puniet |
Power Electronics Aspar | Aprilia | +4.244 |
| 18 |
Hiroshi Aoyama |
Avintia Blusens | FTR | +4.523 |
| 19 |
Michael Laverty |
Paul Bird Motorsport | ART-Aprilia | +5.069 |
| 20 |
Luca Scassa |
Cardion AB Motoracing | Aprilia | +5.331 |
| 21 |
Claudio Corti |
NGM Mobile Forward Racing | Suter | +6.146 |
| 22 |
Héctor Barberá |
Avintia Blusens | FTR | +6.175 |
| 23 | 
Damian Cudlin |
Paul Bird Motorsport | ART-Aprilia | +7.511 |
| 24 |
Bryan Staring |
GO&FUN Honda Gresini | Honda | +9.241 |
| 25 | 
Lukas Pesek |
Came IodaRacing Project | FTR | +9.461 |