Omar Perez's 11th-minute goal gave Santa Fe, who finished fourth in the Apertura first stage, the win at home against the team that finished top.
It leaves Wilson Gutierrez's Santa Fe well-placed heading into the second leg of the semi-final tie, with Junior and Millonarios playing out a 0-0 draw in the other last-four clash.
Atletico Nacional claimed both titles last year but fell behind to the game's only goal early at the Estadio El Campin.
Perez netted into the bottom corner from 10 yards after a cutback,and Santa Fe will carry their lead into Sunday's return leg.
In the other semi-final, visitors Millonarios managed to earn a scoreless draw against Junior at the Estadio Metropolitano Roberto Melendez.
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