| 5. Round | 23/07/2016 | Deportivo Pasto | - | Atlético Junior | 1:1 | ||||
| 8. Round | 13/08/2016 | Atlético Junior | - | Águilas Doradas | 1:1 | ||||
| 10. Round | 28/08/2016 | Atlético Junior | - | Jaguares de Córdoba | 1:0 |  |
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| 7. Round | 04/09/2016 | Jaguares de Córdoba | - | Atlético Junior | 0:0 | |
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| 11. Round | 11/09/2016 | Atlético Junior | - | Fortaleza FC | 1:2 | |
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| 13. Round | 17/09/2016 | Atlético Junior | - | Once Caldas | 0:1 | |
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| 14. Round | 26/09/2016 | Boyacá Chicó | - | Atlético Junior | 2:2 | ||||
| 18. Round | 30/10/2016 | Atlético Junior | - | Envigado FC | 2:1 | |
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| 19. Round | 06/11/2016 | Cortuluá | - | Atlético Junior | 1:2 | |
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| 12. Round | 10/11/2016 | Atlético Nacional | - | Atlético Junior | 2:2 | ||||
| 20. Round | 20/11/2016 | Atlético Junior | - | La Equidad | 2:1 |
Colombia