| 2. Round | 10/07/2016 | Atlético Junior | - | Independiente Medellín | 1:1 | ||||
| 4. Round | 17/07/2016 | Atlético Junior | - | Santa Fe | 2:1 |  |
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| 5. Round | 23/07/2016 | Deportivo Pasto | - | Atlético Junior | 1:1 | ||||
| 6. Round | 30/07/2016 | Atlético Junior | - | Alianza Petrolera | 2:0 | ||||
| 8. Round | 13/08/2016 | Atlético Junior | - | Águilas Doradas | 1:1 | |
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| 9. Round | 21/08/2016 | Deportes Tolima | - | Atlético Junior | 1:1 |  |
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| 10. Round | 28/08/2016 | Atlético Junior | - | Jaguares de Córdoba | 1:0 | ||||
| 11. Round | 11/09/2016 | Atlético Junior | - | Fortaleza FC | 1:2 | |
Colombia