| 7. Round | 15/03/2009 | Atlético Junior | - | Real Cartagena | 0:2 | ||||
| 8. Round | 20/03/2009 | Boyacá Chicó | - | Atlético Junior | 0:0 | ||||
| 9. Round | 22/03/2009 | Real Cartagena | - | Atlético Junior | 0:2 | ||||
| 10. Round | 05/04/2009 | Atlético Junior | - | Santa Fe | 3:1 | ||||
| 12. Round | 19/04/2009 | Atlético Junior | - | Independiente Medellín | 2:1 |  |
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| 14. Round | 30/04/2009 | Atlético Junior | - | La Equidad | 1:1 | |
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| 16. Round | 10/05/2009 | Atlético Junior | - | Atlético Huila | 4:0 |  |
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| 17. Round | 14/05/2009 | Atlético Junior | - | Deportes Quindío | 4:1 | ||||
| 18. Round | 17/05/2009 | Deportes Tolima | - | Atlético Junior | 1:0 |
Colombia