The tournament comprised a total of 36 teams, and the winners were Atlético Nacional, who defeated defending champions Junior 3–1 on aggregate score in the final.
However, neither Atlético Nacional nor Junior earned a berth to the 2017 Copa Sudamericana for having qualified for the Copa Libertadores, with semifinalists Deportes Tolima qualifying instead.
The 8 group winners plus the best 4 second-placed teams joined the teams qualified for the 2016 Copa Libertadores (Deportivo Cali, Atlético Nacional, and Santa Fe) and the previous edition's winners (Junior) in the round of 16, from where the cup continued on a home-and-away knockout basis.
Each tie in the knockout phase was played in a home-and-away two-legged format.
Deportivo Cali, Atlético Nacional, Santa Fe, and Junior entered the competition in the Round of 16, being joined there by the eight group winners and the four best second-placed teams.