| P | Driver | Team | Gap | Grid |
| 1 | Nico Rosberg | Mercedes | 1:26:43.333 | 1 |
| 2 | Max Verstappen | Red Bull Racing | +4.9s | 3 |
| 3 | Lewis Hamilton | Mercedes | +5.7s | 2 |
| 4 | Sebastian Vettel | Scuderia Ferrari | +20.2s | 6 |
| 5 | Kimi Räikkönen | Scuderia Ferrari | +28.3s | 8 |
| 6 | Daniel Ricciardo | Red Bull Racing | +33.9s | 4 |
| 7 | Sergio Perez | Force India | +57.4s | 5 |
| 8 | Nico Hülkenberg | Force India | +59.1s | 9 |
| 9 | Felipe Massa | Williams | +97.7s | 12 |
| 10 | Valtteri Bottas | Williams | +98.3s | 11 |
| 11 | Romain Grosjean | Haas | +99.2s | 7 |
| 12 | Jolyon Palmer | Renault | +1 Lap | 16 |
| 13 | Daniil Kvyat | Toro Rosso | +1 Lap | 13 |
| 14 | Kevin Magnussen | Renault | +1 Lap | 17 |
| 15 | Marcus Ericsson | Sauber | +1 Lap | 18 |
| 16 | Fernando Alonso | McLaren | +1 Lap | 15 |
| 17 | Carlos Sainz | Toro Rosso | +1 Lap | 14 |
| 18 | Jenson Button | McLaren | +1 Lap | 22 |
| 19 | Felipe Nasr | Sauber | +1 Lap | 19 |
| 20 | Esteban Gutierrez | Haas | +1 Lap | 10 |
| 21 | Esteban Ocon | Manor Racing | +1 Lap | 20 |
| 22 | Pascal Wehrlein | Manor Racing | +1 Lap | 21 |
Note: The Mercedes AMG Petronas F1 team secured the 2016 Constructors' title in Japan
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