| P | Rider | Team | Km/h | Time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Jorge Lorenzo | Movistar Yamaha | 283.6 | 01:33.238 | ||||
| 2 | Andrea Iannone | Pramac Racing | 283.3 | 01:33.289 | 0.051 / 0.051 | |||
| 3 | Valentino Rossi | Movistar Yamaha | 283.4 | 01:33.302 | 0.064 / 0.013 | |||
| 4 | Marc Marquez | Repsol Honda | 284.2 | 01:33.360 | 0.122 / 0.058 | |||
| 5 | Dani Pedrosa | Repsol Honda | 286.6 | 01:33.418 | 0.180 / 0.058 | |||
| 6 | Andrea Dovizioso | Ducati | 287.4 | 01:33.439 | 0.201 / 0.021 | |||
| 7 | Pol Espargaro | Tech 3 | 285.0 | 01:33.557 | 0.319 / 0.118 | |||
| 8 | Aleix Espargaro | Forward Racing | 279.8 | 01:33.713 | 0.475 / 0.156 | |||
| 9 | Bradley Smith | Tech 3 | 285.5 | 01:33.761 | 0.523 / 0.048 | |||
| 10 | Stefan Bradl+ | LCR Honda | 287.1 | 01:33.995 | 0.757 / 0.234 | |||
| 11 | Yonny Hernandez+ | Pramac Racing | 281.7 | 01:34.283 | 1.045 / 0.288 | |||
| 12 | Alvaro Bautista | Go&Fun Honda | 283.9 | 01:34.640 | 1.402 / 0.357 |
+Riders advanced from Q1 to Q2
| 13 | Cal Crutchlow | Ducati | 282.6 | 01:34.495 | 0.319 / 0.118 | |||
| 14 | Scott Redding | Go&Fun Honda | 270.6 | 01:34.919 | 0.743 / 0.424 | |||
| 15 | Hiroshi Aoyama | Drive M7 Aspar | 275.2 | 01:34.966 | 0.790 / 0.047 | |||
| 16 | Leon Camier* | Drive M7 Aspar | 269.1 | 01:35.275 | 1.099 / 0.309 | |||
| 17 | Karel Abraham | Cardion AB | 272.9 | 01:35.292 | 1.116 / 0.017 | |||
| 18 | Michael Laverty | Paul Bird | 273.9 | 01:35.589 | 1.413 / 0.297 | |||
| 19 | Alex de Angelis | Forward Racing | 277.9 | 01:35.679 | 1.503 / 0.090 | |||
| 20 | Broc Parkes | Paul Bird | 268.5 | 01:36.317 | 2.141 / 0.638 | |||
| 21 | Hector Barbera | Avintia Racing | 275.7 | 01:36.689 | 2.513 / 0.372 | |||
| 22 | Mike di Meglio | Avintia Racing | 236.3 | 01:42.497 | 8.321 / 5.808 | |||
| 23 | Danilo Petrucci | IodaRacing | no time |
*Substitute for Nicky Hayden
Note: Drive M7 Aspar rider Nicky Hayden was ruled out of the San Marino Grand Prix