| # | Rider | Team | Time | Gap |
|---|---|---|---|---|
| 1 | Manuel Quinziato | Liquigas | 02:46:21 | |
| 2 | Andriy Grivko | Team Milram | + 07 | + 07 |
| 3 | Nicholas White | Team MTN | + 07 | + 07 |
| 4 | Hugo Sabido | Barloworld | + 31 | + 31 |
| 5 | Claudio Corioni | Liquigas | + 01:35 | + 01:35 |
| 6 | Jamie Ball | House of Paint | + 01:35 | + 01:35 |
| 7 | Robert Thomson Jay | Team MTN | + 01:35 | + 01:35 |
| 8 | David O'loughlin | Pezula Racing | + 01:35 | + 01:35 |
| 9 | Daryl Impey | Barloworld | + 01:35 | + 01:35 |
| 10 | Vincenzo Nibali | Liquigas | + 01:39 | + 01:39 |
| 11 | Jacques Janse van Rensburg | Team Neotel | + 01:43 | + 01:43 |
| 12 | Michael Robinson | Intaka Tech - South African DT | + 04:19 | + 04:19 |
| 13 | Michael Sowerby | South Africa | + 05:45 | + 05:45 |
| 14 | Pablo Wilches Juan | Team Konica Minolta - Bizhub | + 06:02 | + 06:02 |
| 15 | Ian Mcleod | Team MTN | + 09:14 | + 09:14 |
| 16 | Artur Gajek | Team Milram | + 09:44 | + 09:44 |
| 17 | Juan van Heerden | Team MTN | + 09:44 | + 09:44 |
| 18 | Ahmed Atunsi Fahti | Libya | + 09:49 | + 09:49 |
| 19 | Travis Allen | Team Konica Minolta - Bizhub | + 09:49 | + 09:49 |
| 20 | Hichem Chaabane | Team Konica Minolta - Bizhub | + 11:56 | + 11:56 |
| 21 | Norberto Wilches | Team Konica Minolta - Bizhub | + 17:54 | + 17:54 |
| 22 | Chris Froome | Barloworld | + 17:54 | + 17:54 |
| 23 | Michael Pepper | South Africa | + 17:54 | + 17:54 |
| 24 | Patrick Calcagni | Barloworld | + 17:54 | + 17:54 |
| 25 | Enrico Gasparotto | Barloworld | + 17:54 | + 17:54 |
| 26 | Diego Caccia | Barloworld | + 17:54 | + 17:54 |
| 27 | Reinardt Janse van Rensburg | Intaka Tech - South African DT | + 17:54 | + 17:54 |
| 28 | Markus Eichler | Team Milram | + 17:54 | + 17:54 |
| 29 | Malcolm Lange | Team MTN | + 17:54 | + 17:54 |
| 30 | David George | Team MTN | + 17:54 | + 17:54 |
| 31 | Hanco Kachelhoffer | House of Paint | + 17:54 | + 17:54 |
| 32 | Christoff van Heerden | Team Konica Minolta - Bizhub | + 17:54 | + 17:54 |
| 33 | Lewis Perry James | Team Neotel | + 17:54 | + 17:54 |
| 34 | Herman Fouche | Team Konica Minolta - Bizhub | + 17:54 | + 17:54 |
| 35 | Johann Rabie | Team Neotel | + 17:54 | + 17:54 |
| 36 | Jaco Venter | Team Neotel | + 17:54 | + 17:54 |
| 37 | Pieter Seyffert | Team Konica Minolta - Bizhub | + 17:54 | + 17:54 |
| 38 | Luthando Kaka | South Africa | + 17:54 | + 17:54 |
| 39 | Marco Velo | Team Milram | + 17:54 | + 17:54 |
| 40 | Peter Velits | Team Milram | + 17:54 | + 17:54 |
| 41 | Leonardo Bertagnolli | Liquigas | + 17:54 | + 17:54 |
| 42 | Björn Schröder | Team Milram | + 17:54 | + 17:54 |
| 43 | Christian Pfannberger | Barloworld | + 17:54 | + 17:54 |
| 44 | Martyn Irvine | Pezula Racing | + 17:54 | + 17:54 |
| 45 | Ciaran Power | Pezula Racing | + 17:54 | + 17:54 |
| 46 | Waylon Woolcock | Team MTN | + 17:54 | + 17:54 |
| 47 | Nolan Hoffman | Team Neotel | + 17:54 | + 17:54 |
| 48 | Dennis van Niekerk | Team Konica Minolta - Bizhub | + 17:54 | + 17:54 |
| 49 | Uwase Nyandwi | Rwanda | + 25:02 | + 25:02 |
| 50 | Nathan Byukusenge | Rwanda | + 25:02 | + 25:02 |
| 51 | Rafiki Uwimana | Rwanda | + 25:02 | + 25:02 |
| 52 | Phetetso Monese | Lesotho | + 25:02 | + 25:02 |
| 53 | Tumisang Taabe | Lesotho | + 25:02 | + 25:02 |
| 54 | Shaban Alsharaa Faysal | Libya | + 25:02 | + 25:02 |
| 55 | Youssef Belgasem Ahmed | Libya | + 25:02 | + 25:02 |
| 56 | Verdi Farao | Intaka Tech - South African DT | + 25:02 | + 25:02 |
| 57 | Mathew Funnell | House of Paint | + 25:02 | + 25:02 |
| 58 | Adam Armstrong | Pezula Racing | + 25:02 | + 25:02 |
| 59 | Adrien Niyonshuti | Rwanda | + 25:02 | + 25:02 |
| 60 | Filippo Pozzato | Liquigas | + 25:02 | + 25:02 |
| 61 | Luca Barla | Team Milram | + 25:02 | + 25:02 |
| 62 | Khalifa Al Mehdi Abdelnasser | Libya | + 25:02 | + 25:02 |
| 63 | Michael van Staden | Intaka Tech - South African DT | + 25:02 | + 25:02 |
| 64 | Kieran Page | Pezula Racing | + 25:02 | + 25:02 |
| 65 | Sebastian Schwager | Team Milram | + 25:02 | + 25:02 |
| 66 | Derek Burke | Pezula Racing | + 25:02 | + 25:02 |
| 67 | Roman Kreuziger | Liquigas | + 25:02 | + 25:02 |
| 68 | Prince Maluleka Wisani | Team Neotel | + 25:02 | + 25:02 |
| 69 | Robert Hunter | Barloworld | + 25:02 | + 25:02 |
| 70 | Morgan Fox | Pezula Racing | + 25:02 | + 25:02 |
| 71 | Lawrence Mashlango | Intaka Tech - South African DT | + 25:02 | + 25:02 |
| 72 | Franco Pellizotti | Liquigas | + 25:02 | + 25:02 |
| 73 | Neil Macdonald | Team MTN | + 25:02 | + 25:02 |
| 74 | Ryan Connor | Pezula Racing | + 25:02 | + 25:02 |
| 75 | Jeremy Maartens | Team Neotel | + 25:02 | + 25:02 |
| 76 | Adrian Maaske | South Africa | + 25:02 | + 25:02 |
| 77 | Richard Baxter | House of Paint | + 25:02 | + 25:02 |
| 78 | Ahadi Seghewir Ali | Libya | + 25:02 | + 25:02 |
| 79 | Lotto Petrus | Team Neotel | + 25:02 | + 25:02 |
| 80 | Jason Bakke | House of Paint | + 25:02 | + 25:02 |
| 81 | Gadi Chait | South Africa | + 25:02 | + 25:02 |
| 82 | Arran Brown | House of Paint | + 25:02 | + 25:02 |
| 83 | Dean Edwards | South Africa | + 25:02 | + 25:02 |
| 84 | Garth Thomas | South Africa | + 25:02 | + 25:02 |
| 85 | Ali Ahmed Mohamed | Libya | + 25:02 | + 25:02 |
| 86 | Stanley Namanyana | Intaka Tech - South African DT | + 25:02 | + 25:02 |
| 87 | Thuso Makatise | Lesotho | + 25:02 | + 25:02 |
| 88 | Poloko Makara | Lesotho | + 25:02 | + 25:02 |
| 89 | Makhashe Ramolungoa | Lesotho | + 25:02 | + 25:02 |
| 90 | Obedi Ruvogera | Rwanda | + 25:02 | + 25:02 |