| # | Rider | Team | Time | Gap |
|---|---|---|---|---|
| 1 | Ivan Basso | Liquigas-Cannondale | 04:01:58 | |
| 2 | Daniel Martin | Garmin - Sharp | + 00 | |
| 3 | Rafal Majka | Saxo Bank - Tinkoff Bank | + 00 | |
| 4 | Julian Arredondo | Team Nippo | + 00 | |
| 5 | Christian Meier | Orica - GreenEDGE | + 46 | + 46 |
| 6 | Miyataka Shimizu | Bridgestone - Anchor | + 59 | + 59 |
| 7 | Simon Clarke | Orica - GreenEDGE | + 59 | + 59 |
| 8 | Christophe Le Mével | Garmin - Sharp | + 01:38 | + 01:38 |
| 9 | Yusuke Hatanaka | Shimano Racing Team | + 01:39 | + 01:39 |
| 10 | Nathan Haas | Garmin - Sharp | + 01:39 | + 01:39 |
| 11 | Masahiro Shinagawa | Aisan Racing Team | + 01:39 | + 01:39 |
| 12 | Taiji Nishitani | Aisan Racing Team | + 01:39 | + 01:39 |
| 13 | Damiano Caruso | Liquigas-Cannondale | + 01:39 | + 01:39 |
| 14 | Tomoyuki Iino | Utsunomiya Blitzen | + 01:39 | + 01:39 |
| 15 | Francois Parisien | Team Spidertech p/b C10 | + 01:39 | + 01:39 |
| 16 | Fumiyuki Beppu | Orica - GreenEDGE | + 01:39 | + 01:39 |
| 17 | Jaroslaw Marycz | Saxo Bank - Tinkoff Bank | + 01:39 | + 01:39 |
| 18 | Nariyuki Masuda | Utsunomiya Blitzen | + 01:41 | + 01:41 |
| 19 | Mark O'brien | Team Budget Forklifts | + 01:41 | + 01:41 |
| 20 | Yoshimitsu Hiratsuka | Shimano Racing Team | + 01:41 | + 01:41 |
| 21 | Masaru Fukuhara | Utsunomiya Blitzen | + 01:41 | + 01:41 |
| 22 | Brian Vandborg | Team Spidertech p/b C10 | + 01:45 | + 01:45 |
| 23 | Ryota Nishizono | Bridgestone - Anchor | + 06:03 | + 06:03 |
| 24 | Ryoma Nonaka | Shimano Racing Team | + 06:03 | + 06:03 |
| 25 | Luis Lemus | Jelly Belly-Kenda | + 06:07 | + 06:07 |
| 26 | Alex Hagman | Jelly Belly-Kenda | + 06:09 | + 06:09 |
| 27 | Yuzuru Suzuki | Shimano Racing Team | + 06:09 | + 06:09 |
| 28 | Ryan Roth | Team Spidertech p/b C10 | + 06:11 | + 06:11 |
| 29 | Takashi Miyazawa | Saxo Bank - Tinkoff Bank | + 06:11 | + 06:11 |
| 30 | Nic Hamilton | Jelly Belly-Kenda | + 06:11 | + 06:11 |
| 31 | Kazuhiro Mori | Aisan Racing Team | + 06:15 | + 06:15 |
| 32 | Kazuo Inoue | Bridgestone - Anchor | + 09:09 | + 09:09 |
| 33 | Ryohei Komori | Team Nippo | + 09:09 | + 09:09 |
| 34 | Suk Lee Ki | + 10:08 | + 10:08 | |
| 35 | Sho Hatsuyama | Utsunomiya Blitzen | + 10:08 | + 10:08 |
| 36 | Makoto Nakamura | Utsunomiya Blitzen | + 10:08 | + 10:08 |
| 37 | Yasuharu Nakajima | Aisan Racing Team | + 10:08 | + 10:08 |
| 38 | Takayuki Abe | Shimano Racing Team | + 10:08 | + 10:08 |
| 39 | Michael Cupitt | Team Budget Forklifts | + 12:44 | + 12:44 |