Carlos Torres Pizarro scored the opening goal before Colombia were allowed back into it before half-time, Felipe Mendez Rojas equalising.
But a late free-kick from Marcelo Medina gave the hosts a 2-1 victory.
Later that night in Paysandú, Paraguay hammered Honduras 4-0 with Nicolás García getting a hat-trick.
But the highlight of the night was a solo run from Paraguayan winger Fernando Paez, who ran 50 yards to score the fifth.
