| 2. Round | 10/07/2016 | Atlético Junior | - | Independiente Medellín | 1:1 | ||||
| 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 | ||||
| 9. Round | 21/08/2016 | Deportes Tolima | - | Atlético Junior | 1:1 | ||||
| 10. Round | 28/08/2016 | Atlético Junior | - | Jaguares de Córdoba | 1:0 | ||||
| 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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| 13. Round | 17/09/2016 | Atlético Junior | - | Once Caldas | 0:1 | ||||
| 12. Round | 10/11/2016 | Atlético Nacional | - | Atlético Junior | 2:2 |
Colombia