| 9. Round | 21/08/2016 | Deportes Tolima | - | Atlético Junior | 1:1 |  |
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| 7. Round | 04/09/2016 | Jaguares de Córdoba | - | Atlético Junior | 0:0 | ||||
| 1. Round | 08/09/2016 | Atlético Huila | - | Atlético Junior | 3:1 | ||||
| 11. Round | 11/09/2016 | Atlético Junior | - | Fortaleza FC | 1:2 |  |
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| 14. Round | 26/09/2016 | Boyacá Chicó | - | Atlético Junior | 2:2 | |
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| 16. Round | 15/10/2016 | Atlético Bucaramanga | - | Atlético Junior | 3:0 | |
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| 17. Round | 22/10/2016 | Deportivo Cali | - | Atlético Junior | 2:0 |  |
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| 20. Round | 20/11/2016 | Atlético Junior | - | La Equidad | 2:1 | |
Chile