| # | Rider | Team | Time | Gap |
|---|---|---|---|---|
| 1 | Michael Rogers | Team Saxo - Tinkoff | 04:25:00 | |
| 2 | Jack Bauer | Garmin - Sharp | + 44 | + 44 |
| 3 | Damiano Cunego | Lampre-Merida | + 44 | + 44 |
| 4 | Julian Arredondo | Team Nippo - De Rosa | + 44 | + 44 |
| 5 | David López | Sky ProCycling | + 50 | + 50 |
| 6 | Manuele Mori | Lampre-Merida | + 58 | + 58 |
| 7 | Joe Dombrowski | Sky ProCycling | + 58 | + 58 |
| 8 | Carlos Verona | Omega Pharma - Quick Step | + 58 | + 58 |
| 9 | Taiji Nishitani | Aisan Racing Team | + 01:05 | + 01:05 |
| 10 | Joshua Edmondson | Sky ProCycling | + 01:33 | + 01:33 |
| 11 | Elia Favilli | Lampre-Merida | + 02:30 | + 02:30 |
| 12 | Ben Hermans | RadioShack-Leopard | + 02:55 | + 02:55 |
| 13 | Pieter Serry | Omega Pharma - Quick Step | + 02:59 | + 02:59 |
| 14 | Ivan Basso | Cannondale Pro Cycling | + 02:59 | + 02:59 |
| 15 | Steele Von Hoff | Garmin - Sharp | + 03:58 | + 03:58 |
| 16 | Serghei Tvetcov | Jelly Belly-Kenda | + 03:58 | + 03:58 |
| 17 | Tomoyuki Iino | Utsunomiya Blitzen | + 03:58 | + 03:58 |
| 18 | Vicente Toribio Jose | Team Ukyo | + 03:58 | + 03:58 |
| 19 | Ryoma Nonaka | Shimano Racing Team | + 03:58 | + 03:58 |
| 20 | Yoshimitsu Hiratsuka | Aisan Racing Team | + 03:58 | + 03:58 |
| 21 | Matthias Krizek | Cannondale Pro Cycling | + 03:58 | + 03:58 |
| 22 | Rory Sutherland | Team Saxo - Tinkoff | + 03:58 | + 03:58 |
| 23 | Daniel Martin | Garmin - Sharp | + 04:04 | + 04:04 |
| 24 | Evgeni Petrov | Team Saxo - Tinkoff | + 04:04 | + 04:04 |
| 25 | Ryota Nishizono | Champion System | + 04:36 | + 04:36 |
| 26 | Hossein Alizadeh | Amore & Vita | + 06:51 | + 06:51 |
| 27 | Naoya Uchino | + 08:10 | + 08:10 | |
| 28 | Sean Mazich | Jelly Belly-Kenda | + 08:17 | + 08:17 |
| 29 | Bernhard Eisel | Sky ProCycling | + 08:17 | + 08:17 |
| 30 | Nariyuki Masuda | Cannondale Pro Cycling | + 08:17 | + 08:17 |
| 31 | Yasuharu Nakajima | Aisan Racing Team | + 08:17 | + 08:17 |
| 32 | Brad Huff | Jelly Belly-Kenda | + 08:17 | + 08:17 |
| 33 | Sho Hatsuyama | Bridgestone - Anchor | + 08:19 | + 08:19 |
| 34 | Naoya Yoshioka | + 08:19 | + 08:19 | |
| 35 | Hayato Yoshida | Shimano Racing Team | + 08:19 | + 08:19 |
| 36 | Uri Martins | Amore & Vita | + 11:26 | + 11:26 |
| 36 | Yuzuru Suzuki | Shimano Racing Team | + 10:30 | + 10:30 |
| 37 | Yuya Akimaru | + 12:16 | + 12:16 | |
| 38 | Shinichi Fukushima | Team Nippo - De Rosa | + 12:36 | + 12:36 |