| # | Rider | Team | Time | Gap |
|---|---|---|---|---|
| 1 | Nathan Haas | Genesys Wealth Advisers | 04:08:35 | |
| 2 | Taiji Nishitani | Aisan Racing Team | + 00 | |
| 3 | Junya Sano | D'Angelo & Antenucci - Nippo | + 00 | |
| 4 | Damiano Cunego | Lampre-ISD | + 00 | |
| 5 | Yusuke Hatanaka | Shimano Racing Team | + 00 | |
| 6 | Manuele Mori | Lampre-ISD | + 02 | + 02 |
| 7 | Damiano Caruso | Liquigas-Cannondale | + 02 | + 02 |
| 8 | Miyataka Shimizu | Bridgestone - Anchor | + 04 | + 04 |
| 9 | Cristiano Salerno | Liquigas-Cannondale | + 07 | + 07 |
| 10 | Ivan Basso | Liquigas-Cannondale | + 09 | + 09 |
| 11 | Yukiya Arashiro | Team Europcar | + 09 | + 09 |
| 12 | Takashi Miyazawa | Farnese Vini - Neri Sottoli | + 30 | + 30 |
| 13 | Ryota Nishizono | Shimano Racing Team | + 30 | + 30 |
| 14 | Shinichi Fukushima | Terengganu Cycling Team | + 30 | + 30 |
| 15 | Yukihiro Doi | Skil - Shimano | + 30 | + 30 |
| 16 | Vincenzo Garofalo | Matrix Powertag | + 30 | + 30 |
| 17 | Masahiro Shinagawa | Aisan Racing Team | + 30 | + 30 |
| 18 | Gustav Larsson | Saxo Bank - SunGard | + 30 | + 30 |
| 19 | Andrey Mizurov | Astana | + 30 | + 30 |
| 20 | Alexandre Shushemoin | Astana | + 30 | + 30 |
| 21 | Makoto Nakamura | Utsunomiya Blitzen | + 30 | + 30 |
| 22 | Nic Hamilton | Jelly Belly-Kenda | + 47 | + 47 |
| 23 | Masaru Fukuhara | Bridgestone - Anchor | + 52 | + 52 |
| 24 | Rafal Majka | Saxo Bank - SunGard | + 01:33 | + 01:33 |
| 25 | Kenichi Suzuki | Aisan Racing Team | + 02:27 | + 02:27 |
| 26 | Yuzuru Suzuki | Shimano Racing Team | + 03:33 | + 03:33 |
| 27 | Mariusz Wiesiak | Matrix Powertag | + 04:37 | + 04:37 |
| 28 | Josep Jufré | Astana | + 04:37 | + 04:37 |
| 29 | Henry Frusto | D'Angelo & Antenucci - Nippo | + 04:37 | + 04:37 |
| 30 | Steele Von Hoff | Genesys Wealth Advisers | + 04:37 | + 04:37 |
| 31 | Kazuo Inoue | Bridgestone - Anchor | + 04:37 | + 04:37 |
| 32 | Tomoya Kano | Bridgestone - Anchor | + 04:37 | + 04:37 |
| 33 | Shinri Suzuki | Shimano Racing Team | + 06:43 | + 06:43 |
| 34 | Kazuki Aoyanagi | Shimano Racing Team | + 07:07 | + 07:07 |
| 35 | Ryohei Komori | D'Angelo & Antenucci - Nippo | + 07:11 | + 07:11 |
| 36 | Yoshimasa Hirose | Utsunomiya Blitzen | + 09:29 | + 09:29 |
| 37 | Akira Kakinuma | Utsunomiya Blitzen | + 09:29 | + 09:29 |
| 38 | Kazuyuki Manabe | Matrix Powertag | + 09:29 | + 09:29 |
| 39 | Yoshiyuki Shimizu | Bridgestone - Anchor | + 09:29 | + 09:29 |
| 40 | Ran Margaliot | Saxo Bank - SunGard | + 09:29 | + 09:29 |
| 41 | Daisei Nagara | Matrix Powertag | + 09:29 | + 09:29 |
| 42 | Tomohiro Hayakawa | + 09:29 | + 09:29 |