Levir Culpi's men were pointless in Group One heading to Bogota, but Pratto's goal just before the hour-mark secured their win.
Pratto headed in a corner from Sherman Cardenas in the 59th minute to see Mineiro to victory at the Estadio Nemesio Camacho El Campin.
It tightened Group One up, with Colo Colo and Santa Fe on six points – and Atlas and Mineiro both on three.
Argentine side Estudiantes went top of Group Seven after a hard-fought 1-0 victory at home to Libertad.
Guido Carrillo scored the winner in the 80th minute, taking a cross from Carlos Auzqui before turning and finishing smartly from close range.
Libertad are second in Group Seven, two points clear of Atletico Nacional and well ahead of point-less Barcelona.
Group Four pacesetters Emelec and Internacional played out a 1-1 draw, with the former playing most of the second half with 10 men.
Sao Paulo made it back-to-back wins thanks to Michel Bastos, who scored a late winner to secure a 1-0 victory over San Lorenzo.
Bastos headed in a Carlinhos cross in the 90th minute to see the Brazilians to their win.
Deportivo Tachira and Guarani traded penalties in their 1-1 draw in Group Eight.
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