| 1 | Peter Sagan (Svk) Tinkoff Team | 1:22:02 | |
| 2 | Sho Hatsuyuma (Jpn) Bridgestone Anchor Cycling Team | ||
| 3 | Christopher Froome (GBr) Team Sky | ||
| 4 | Adam Yates (GBr) Orica-BikeExchange | 0:00:05 | |
| 5 | Marcel Kittel (Ger) Etixx – Quick-Step | 0:00:12 | |
| 6 | Samuel Dumoulin (Fra) AG2R La Mondiale | ||
| 7 | Fumiyuki Beppu (Jpn) Trek-Segafredo | ||
| 8 | Shimpei Fukuda (Jpn) Aisan Racing Team | ||
| 9 | Zico Waeytens (Bel) Team Giant-Alpecin | ||
| 10 | Romain Bardet (Fra) AG2R La Mondiale | ||
| 11 | Koen De Kort (Ned) Team Giant-Alpecin | ||
| 12 | Takeaki Ayabe (Jpn) Aisan Racing Team | ||
| 13 | Hayato Okamoto (Jpn) Japan | ||
| 14 | Daisuke Kaneko (Jpn) Matrix Powertag | ||
| 15 | Fabio Sabatini (Ita) Etixx – Quick-Step | ||
| 16 | Alexis Vuillermoz (Fra) AG2R La Mondiale | ||
| 17 | Eiya Hashimoto (Jpn) Japan | ||
| 18 | Kazuki Kobayashi (Jpn) Japan | ||
| 19 | Rafal Majka (Pol) Tinkoff Team | ||
| 20 | Hideto Nakane (Jpn) Aisan Racing Team | ||
| 21 | Georg Preidler (Aut) Team Giant-Alpecin | 0:00:18 | |
| 22 | Ryohei Komori (Jpn) Aisan Racing Team | ||
| 23 | Julien Vermote (Bel) Etixx – Quick-Step | ||
| 24 | Mikaël Cherel (Fra) AG2R La Mondiale | ||
| 25 | Yuya Amikaru (Jpn) Shimano Racing Team | ||
| 26 | Wouter Poels (Ned) Team Sky | ||
| 27 | Ian Boswell (USA) Team Sky | ||
| 28 | Simon Gerrans (Aus) Orica-BikeExchange | ||
| 29 | Simon Geschke (Ger) Team Giant-Alpecin | ||
| 30 | Michael Kolar (Svk) Tinkoff Team | ||
| 31 | Pawel Poljanski (Pol) Tinkoff Team | ||
| 32 | Petr Vakoc (Cze) Etixx – Quick-Step | ||
| 33 | Christopher Juul Jensen (Den) Orica-BikeExchange | ||
| 34 | Christian Meier (Can) Orica-BikeExchange | ||
| 35 | Yukiya Arashiro (Jpn) Lampre – Merida | ||
| 36 | Kohei Uchima (Jpn) Bridgestone Anchor Cycling Team | ||
| 37 | Michal Golas (Pol) Team Sky | ||
| 38 | Ryu Suzuki (Jpn) Bridgestone Anchor Cycling Team | ||
| 39 | Yuri Kobashi (Jpn) Shimano Racing Team | ||
| 40 | Yuma Koishi (Jpn) Nippo – Vini Fantini | ||
| 41 | Ryota Nishizono (Jpn) Bridgestone Anchor Cycling Team | ||
| 42 | Taisei Kobayashi (Jpn) Japan | ||
| 43 | Kazushige Kuboki (Jpn) Nippo – Vini Fantini | ||
| 44 | Manabu Shibashi (Jpn) Nippo – Vini Fantini | ||
| 45 | Marino Kobayashi (Jpn) Nippo – Vini Fantini | ||
| 46 | Shigetomo Nakanishi (Jpn) Korail Cycling Team | ||
| 47 | Keisuke Kimura (Jpn) Shimano Racing Team | ||
| 48 | Kosuke Aso (Jpn) Korail Cycling Team | ||
| 49 | Kenji Itami (Jpn) Korail Cycling Team | ||
| 50 | Satoshi Nakagawa (Jpn) Matrix Powertag | ||
| DNF | Ryosuke Hashimoto (Jpn) Matrix Powertag |
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