Andres Mosquera's header in the 89th minute saw Medellin equalise at 1-1 in the second leg of the final but the visitors were unable to reel in Santa Fe, who triumphed 3-2 on aggregate to notch their first title since the 2012 Apertura.
Luis Carlos Arias' 30-yard drive for Santa Fe in the first minute after half-time would prove the difference at the Estadio Nemesio Camacho.
Medellin's best chance to level the final at 3-3 on aggregate came in stoppage time but Santa Fe goalkeeper Camilo Vargas saved Christian Marrugo's header.
Having won the first leg in Medellin 2-1 on Wednesday, Santa Fe started their home leg in prime position to clinch the Clausura title.
Santa Fe sat back for the majority of the match as Medellin attempted to level the tie on aggregate with the visitors accumulating 63 per cent possession but could not break down the hosts' defence.
The home side produced just one shot on target but it was enough with Arias blasting a left-foot shot into the bottom corner in the 46th minute.
Medellin eventually found a goal with Vladimir Marin's cross picking out Diego Herner at the back post and his header was nodded into the net by Mosquera.
The visitors grabbed the ball and sprinted back to the middle to ensure a prompt restart but they were unable to score the goal that would have forced a penalty shoot-out.
