| P | Rider | Team | Km/h | Time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Yonny Hernandez | Pramac Racing | 271.9 | 01:50.310 | ||||
| 2 | Marc Marquez | Repsol Honda | 274.7 | 01:52.003 | 1.693 / 1.693 | |||
| 3 | Andrea Dovizioso | Ducati | 275.6 | 01:52.093 | 1.783 / 0.090 | |||
| 4 | Stefan Bradl | LCR Honda | 264.9 | 01:52.386 | 2.076 / 0.293 | |||
| 5 | Danilo Petrucci | IodaRacing | 263.0 | 01:53.157 | 2.847 / 0.771 | |||
| 6 | Aleix Espargaro | Forward Racing | 262.3 | 01:53.336 | 3.026 / 0.179 | |||
| 7 | Andrea Iannone | Pramac Racing | 259.1 | 01:53.478 | 3.168 / 0.142 | |||
| 8 | Pol Espargaro | Tech 3 | 266.6 | 01:53.765 | 3.455 / 0.287 | |||
| 9 | Valentino Rossi | Movistar Yamaha | 269.7 | 01:54.243 | 3.933 / 0.478 | |||
| 10 | Dani Pedrosa | Repsol Honda | 258.4 | 01:54.450 | 4.140 / 0.207 | |||
| 11 | Alex de Angelis | Forward Racing | 250.7 | 01:55.063 | 4.753 / 0.613 | |||
| 12 | Jorge Lorenzo | Movistar Yamaha | 265.0 | 01:55.415 | 5.105 / 0.352 | |||
| 13 | Cal Crutchlow | Ducati | 264.1 | 01:56.650 | 6.340 / 1.235 | |||
| 14 | Karel Abraham | Cardion AB | 259.7 | 01:56.716 | 6.406 / 0.066 | |||
| 15 | Michael Laverty | Paul Bird | 258.6 | 01:56.732 | 6.422 / 0.016 | |||
| 16 | Scott Redding | Go&Fun Honda | 249.1 | 01:56.776 | 6.466 / 0.044 | |||
| 17 | Alvaro Bautista | Go&Fun Honda | 251.8 | 01:56.830 | 6.520 / 0.054 | |||
| 18 | Hiroshi Aoyama | Drive M7 Aspar | 258.6 | 01:58.769 | 8.459 / 1.939 | |||
| 19 | Mike di Meglio | Avintia Racing | 240.2 | 02:01.914 | 11.604 / 3.145 | |||
| 20 | Leon Camier* | Drive M7 Aspar | 235.0 | 02:02.600 | 12.290 / 0.686 | |||
| 21 | Hector Barbera | Avintia Racing | 233.4 | 02:06.903 | 16.593 / 4.303 | |||
| 22 | Broc Parkes | Paul Bird | no time | |||||
| 23 | Bradley Smith | Tech 3 | no time |
*Substitute for Nicky Hayden
Note: Drive M7 Aspar rider Nicky Hayden was ruled out of the San Marino Grand Prix