| Pos. | Num. | Rider | Nation | Team | Motorcycle | Lap time | Km/h | Gap |
| 1 | 3 | Dani PEDROSA | SPA | Repsol Honda Team | Honda | 2’01.427 | 314.318 | |
| 2 | 46 | Valentino ROSSI | ITA | Fiat Yamaha Team | Yamaha | 2’01.446 | 309.544 | 0.019 |
| 3 | 27 | Casey STONER | AUS | Ducati Marlboro Team | Ducati | 2’01.485 | 309.988 | 0.058 |
| 4 | 99 | Jorge LORENZO | SPA | Fiat Yamaha Team | Yamaha | 2’01.804 | 309.189 | 0.377 |
| 5 | 4 | Andrea DOVIZIOSO | ITA | Repsol Honda Team | Honda | 2’02.076 | 307.079 | 0.649 |
| 6 | 24 | Toni ELIAS | SPA | San Carlo Honda Gresini | Honda | 2’02.181 | 311.059 | 0.754 |
| 7 | 69 | Nicky HAYDEN | USA | Ducati Marlboro Team | Ducati | 2’02.416 | 309.455 | 0.989 |
| 8 | 5 | Colin EDWARDS | USA | Monster Yamaha Tech 3 | Yamaha | 2’02.425 | 306.992 | 0.998 |
| 9 | 36 | Mika KALLIO | FIN | Pramac Racing | Ducati | 2’02.607 | 311.059 | 1.180 |
| 10 | 65 | Loris CAPIROSSI | ITA | Rizla Suzuki MotoGP | Suzuki | 2’02.825 | 309.278 | 1.398 |
| 11 | 14 | Randy DE PUNIET | FRA | LCR Honda MotoGP | Honda | 2’02.993 | 305.689 | 1.566 |
| 12 | 7 | Chris VERMEULEN | AUS | Rizla Suzuki MotoGP | Suzuki | 2’03.181 | 305.343 | 1.754 |
| 13 | 15 | Alex DE ANGELIS | RSM | San Carlo Honda Gresini | Honda | 2’03.220 | 305.949 | 1.793 |
| 14 | 44 | Aleix ESPARGARO | SPA | Pramac Racing | Ducati | 2’03.458 | 305.689 | 2.031 |
| 15 | 33 | Marco MELANDRI | ITA | Hayate Racing Team | Kawasaki | 2’03.732 | 308.307 | 2.305 |
| 16 | 52 | James TOSELAND | GBR | Monster Yamaha Tech 3 | Yamaha | 2’04.078 | 302.351 | 2.651 |
| 17 | 41 | Gabor TALMACSI | HUN | Scot Racing Team MotoGP | Honda | 2’04.492 | 304.654 | 3.065 |
MotoGP Malaysia 2009: Second Practice Times
October 24, 2009
