| Group A | 20/08/2016 | FBC Melgar | - | Universidad Cesar Vallejo | 1:0 | ||||
| Group A | 25/08/2016 | Unión Comercio | - | FBC Melgar | 0:0 |  |
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| Group A | 11/09/2016 | FBC Melgar | - | Deportivo Municipal | 2:1 | ||||
| Group A | 25/09/2016 | FBC Melgar | - | Defensor La Bocana | 1:0 | |
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| Group A | 16/10/2016 | FBC Melgar | - | Sporting Cristal | 2:0 | |
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| Group A | 19/10/2016 | Universidad Cesar Vallejo | - | FBC Melgar | 2:3 |  |
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| Group A | 24/10/2016 | FBC Melgar | - | Unión Comercio | 1:0 | |
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| Group A | 29/10/2016 | Deportivo Municipal | - | FBC Melgar | 0:0 | ||||
| Group A | 02/11/2016 | FBC Melgar | - | Real Garcilaso | 0:0 | |
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| Group A | 22/11/2016 | FBC Melgar | - | Juan Aurich | 1:2 | |
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| Group A | 27/11/2016 | Sporting Cristal | - | FBC Melgar | 3:2 |
Uruguay