| 9. Jornada | 21.08.2016 | Deportes Tolima | - | Atlético Junior | 1:1 |  |
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| 7. Jornada | 04.09.2016 | Jaguares de Córdoba | - | Atlético Junior | 0:0 | ||||
| 1. Jornada | 08.09.2016 | Atlético Huila | - | Atlético Junior | 3:1 | ||||
| 11. Jornada | 11.09.2016 | Atlético Junior | - | Fortaleza FC | 1:2 |  |
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| 14. Jornada | 26.09.2016 | Boyacá Chicó | - | Atlético Junior | 2:2 | |
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| 16. Jornada | 16.10.2016 | Atlético Bucaramanga | - | Atlético Junior | 3:0 | |
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| 17. Jornada | 23.10.2016 | Deportivo Cali | - | Atlético Junior | 2:0 |  |
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| 20. Jornada | 20.11.2016 | Atlético Junior | - | La Equidad | 2:1 | |
Chile