Following a goalless draw in the first leg in Medellin on Sunday, the title was up for grabs at Santa Fe's Estadio Nemesio Camacho in Bogota on Wednesday.
And it was the visitors who drew first blood seven minutes before half-time, with striker Jefferson Duque charging into the box, beating two defenders before rifling a right-foot shot between the legs of Santa Fe goalkeeper Camilo Vargas.
Atletico had to wait until the 83rd minute to make sure of victory, however, and the goal came courtesy of substitute Luis Mosquera.
Mosquera, who replaced Duque on 79 minutes, made sure of the win when he collected a pass inside the box and his side-footed effort found its way past Vargas and into the net, securing Atletico their 12th Colombian title.
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