The first leg ended in a 1-0 win for Medellin, who face the task of defending that league in the second leg played at their own Atanasio Girardot stadium.
Things initially did not go according to plan for Medellin, who had difficulties controlling the match in the first half and conceded a goal in the 42nd minute when Ervin Maturana headed home from a corner kick.
But the hosts did take much the initiative in the second half, and an effort from Jackson Martinez went in from the post on 68 minutes.
Four minutes later, Luis Mosquera made it 2-1 as he found the smallest of gaps to put the ball past the opposing goalkeeper. The player was booked for losing his shirt in the following celebrations.
Huila did pull one back through Lewis Ocha in the 83rd minute, but Medellin held on to their aggregate lead to secure their fifth Colombian championship.
DIM won their first national trophy in 1955, followed by victories in 1957, 2002 and 2004.