| Clt | N° | Pilote | Team | Machine | Temps | Moyenne | Ecart |
| 1er | 44 | Pol ESPARGARO (SPA) | Tuenti Racing | DERBI | 41’52.280 | 143.926 | |
| 2e | 40 | Nicolas TEROL (SPA) | Bancaja Aspar Team | APRILIA | 41’53.237 | 143.871 | 0.957 |
| 3e | 93 | Marc MARQUEZ (SPA) | Red Bull Ajo Motosport | DERBI | 41’56.708 | 143.673 | 4.428 |
| 4e | 7 | Efren VAZQUEZ (SPA) | Tuenti Racing | DERBI | 41’57.016 | 143.655 | 4.736 |
| 5e | 38 | Bradley SMITH (GBR) | Bancaja Aspar Team | APRILIA | 41’57.423 | 143.632 | 5.143 |
| 6e | 11 | Sandro CORTESE (GER) | Avant Mitsubishi Ajo | DERBI | 41’58.127 | 143.592 | 5.847 |
| 7e | 12 | Esteve RABAT (SPA) | Blusens STX | APRILIA | 42’03.327 | 143.296 | 11.047 |
| 8e | 71 | Tomoyoshi KOYAMA (JPN) | Racing Team Germany | APRILIA | 42’03.445 | 143.289 | 11.165 |
| 9e | 99 | Danny WEBB (GBR) | Andalucia Cajasol | APRILIA | 42’30.088 | 141.792 | 37.808 |
| 10e | 39 | Luis SALOM (SPA) | Stipa Molenaar Racing GP | APRILIA | 42’31.865 | 141.694 | 39.585 |
| 11e | 14 | Johann ZARCO (FRA) | WTR San Marino Team | APRILIA | 42’32.799 | 141.642 | 40.519 |
| 12e | 53 | Jasper IWEMA (NED) | CBC Corse | APRILIA | 42’33.097 | 141.625 | 40.817 |
| 13e | 94 | Jonas FOLGER (GER) | Ongetta Team | APRILIA | 42’34.429 | 141.551 | 42.149 |
| 14e | 35 | Randy KRUMMENACHE (SWI) | Stipa Molenaar Racing GP | APRILIA | 42’37.021 | 141.408 | 44.741 |
| 15e | 26 | Adrian MARTIN (SPA) | Aeroport de Castello Ajo | APRILIA | 42’38.600 | 141.321 | 46.320 |
| 16e | 5 | Alexis MASBOU (FRA) | Ongetta Team | APRILIA | 42’38.783 | 141.310 | 46.503 |
| 17e | 23 | Alberto MONCAYO (SPA) | Andalucia Cajasol | APRILIA | 42’39.259 | 141.284 | 46.979 |
| 18e | 78 | Marcel SCHROTTER (GER) | Interwetten Honda 125 | HONDA | 42’51.906 | 140.589 | 59.626 |
| 19e | 84 | Jakub KORNFEIL (CZE) | Racing Team Germany | APRILIA | 42’52.050 | 140.582 | 59.770 |
| 20e | 50 | Sturla FAGERHAUG (NOR) | AirAsia Sepang Int Circuit | APRILIA | 42’56.685 | 140.329 | 1’04.405 |
| 21e | 69 | Louis ROSSI (FRA) | CBC Corse | APRILIA | 42’58.011 | 140.256 | 1’05.731 |
| 22e | 60 | Michael VAN DER MARK (NED) | Lambretta Reparto Corse | LAMBRETTA | 43’21.208 | 139.006 | 1’28.928 |
| 23e | 82 | Kevin SZALAI (FRA) | Equipe France Vitesse Espoir | HONDA | 43’39.423 | 138.039 | 1’47.143 |
| 24e | 81 | Gregory DI CARLO (FRA) | Equipe France Vitesse Espoir | HONDA | 41’53.349 | 137.871 | 1 tour |
| 25e | 63 | Zulfahmi KHAIRUDDIN (MAL) | AirAsia Sepang Int Circuit | APRILIA | 42’19.286 | 136.462 | 1 tour |
| 26e | 83 | Morgan BERCHET (FRA) | Xtreme Racing Team | HONDA | 42’53.487 | 134.649 | 1 tour |