After conceding a lead last time out to lose 2-1 at home to Santa Fe, Wilson Gutierrez's men recovered from an early concession to earn all three points at the Estadio Departamental Libertad.
Former Aston Villa striker Juan Pablo Angel put Atletico ahead in the ninth minute, but Juan Osorio's men would miss the chance to climb to fourth as the home side fought back.
Jairo Patino equalised in the 35th minute, before Equatorial Guinea international Mauricio Mina scored what would be the winner in the 67th minute.
It was a necessary return to form for Pasto, who had lost two in a row, while Atletico have now been beaten in their past two, and have one win in seven in all competitions.
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