| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Andrea Dovizioso | Ducati | 293.5 | 01:33.338 | ||||
| 2 | Marc Marquez | Repsol Honda | 290.7 | 01:33.446 | 0.108 / 0.108 | |||
| 3 | Maverick Viñales | Movistar Yamaha | 293.9 | 01:33.527 | 0.189 / 0.081 | |||
| 4 | Jorge Lorenzo | Ducati | 293.8 | 01:33.555 | 0.217 / 0.028 | |||
| 5 | Alvaro Bautista | Pull&Bear Aspar | 293.4 | 01:33.934 | 0.596 / 0.379 | |||
| 6 | Dani Pedrosa | Repsol Honda | 293.7 | 01:33.939 | 0.601 / 0.005 | |||
| 7 | Cal Crutchlow | LCR Honda | 291.9 | 01:34.092 | 0.754 / 0.153 | |||
| 8 | Johann Zarco | Tech 3 | 291.4 | 01:34.125 | 0.787 / 0.033 | |||
| 9 | Jonas Folger | Tech 3 | 289.9 | 01:34.176 | 0.838 / 0.051 | |||
| 10 | Danilo Petrucci | Octo Pramac Racing | 291.6 | 01:34.237 | 0.899 / 0.061 | |||
| 11 | Aleix Espargaro | Aprilia Gresini | 290.3 | 01:34.251 | 0.913 / 0.014 | |||
| 12 | Tito Rabat | EG 0,0 Marc VDS | 290.0 | 01:34.381 | 1.043 / 0.130 | |||
| 13 | Michele Pirro* | Ducati | 293.0 | 01:34.426 | 1.088 / 0.045 | |||
| 14 | Jack Miller | EG 0,0 Marc VDS | 290.0 | 01:34.455 | 1.117 / 0.029 | |||
| 15 | Loris Baz | Reale Avintia Racing | 287.1 | 01:34.606 | 1.268 / 0.151 | |||
| 16 | Andrea Iannone | Suzuki Ecstar | 288.3 | 01:34.688 | 1.350 / 0.082 | |||
| 17 | Pol Espargaro | Red Bull KTM | 292.6 | 01:34.695 | 1.357 / 0.007 | |||
| 18 | Scott Redding | Octo Pramac Racing | 288.7 | 01:34.852 | 1.514 / 0.157 | |||
| 19 | Bradley Smith | Red Bull KTM | 289.0 | 01:35.109 | 1.771 / 0.257 | |||
| 20 | Alex Rins | Suzuki Ecstar | 290.1 | 01:35.128 | 1.790 / 0.019 | |||
| 21 | Sam Lowes | Aprilia Gresini | 285.1 | 01:35.149 | 1.811 / 0.021 | |||
| 22 | Karel Abraham | Pull&Bear Aspar | 290.0 | 01:35.150 | 1.812 / 0.001 | |||
| 23 | Hector Barbera | Reale Avintia Racing | 295.6 | 01:35.260 | 1.922 / 0.110 |
*Wild card entry
Note: Movistar Yamaha MotoGP rider Valentino Rossi did not take part in the San Marino Grand Prix after breaking his tibia and fibula in a training crash