It was all on the line at Atletico Nacional after the first leg finished 0-0 between the two sides in Cali.
After 17 minutes, Nestor Camacho deflected a harmless header from a corner into his own net to give Atletico the lead.
Atletico pushed hard for a second goal and were rewarded on 62 minutes as Cali were caught on the break.
A goal kick was flicked on and Jefferson Duque's first touch took him around the goalkeeper to seal the championship.
It is Atletico's 13th Colombian championship – taking them to within one of Millonarios' 14 titles.
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