Olimpia reach Libertadores final despite defeat
Striker Wilder Medina scored the only goal at El Campin stadium in the 75th minute but the Colombian side's poor finishing denied them the chance to reach their first final.
Santa Fe midfielder Omar Perez's free-kick came back off the woodwork and Medina was on hand to score despite goalkeeper Martin Silva's last-ditch effort to prevent the ball from crossing his line.
Olimpia, who won their third and last title in South America's elite club tournament in 2002, were on the defensive for most of the match, going through thanks to their 2-0 first leg win in Asuncion last week.
Santa Fe came closest to levelling the tie when Cristian Martinez Borja's shot hit the post six minutes from time.