| 1. Round | 29/01/2012 | Atlético Junior | - | Deportes Quindío | 1:1 | ||||
| 3. Round | 12/02/2012 | Deportivo Pasto | - | Atlético Junior | 1:1 |  |
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| 4. Round | 18/02/2012 | Atlético Junior | - | Deportivo Cali | 1:0 | ||||
| 6. Round | 03/03/2012 | Atlético Junior | - | Itagüi Ditaires | 2:1 | ||||
| 7. Round | 11/03/2012 | Patriotas FC | - | Atlético Junior | 2:1 | |
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| 8. Round | 17/03/2012 | Atlético Junior | - | Boyacá Chicó | 3:1 | ||||
| 9. Round | 25/03/2012 | Atlético Junior | - | Real Cartagena | 3:1 | ||||
| 10. Round | 01/04/2012 | Santa Fe | - | Atlético Junior | 2:1 | ||||
| 12. Round | 15/04/2012 | Atlético Huila | - | Atlético Junior | 1:3 | ||||
| 13. Round | 22/04/2012 | Atlético Junior | - | Deportes Tolima | 1:2 | ||||
| 16. Round | 14/05/2012 | Atlético Nacional | - | Atlético Junior | 3:1 | ||||
| 18. Round | 27/05/2012 | Once Caldas | - | Atlético Junior | 2:2 |
Colombia