Atletico went ahead in the 20th minute on Thursday when Diego Tardelli's shot came back off the bar and Fernandinho lifted the ball over a defender inside the box before rifling a volley inside Franco Armani’s far post.
The Colombian side equalised in the 88th minute when Atletico goalkeeper Victor failed to intercept a low cross from the left and Duque slid in at the far post to steer the ball home.
“We’re sad not to have qualified but at the same time the standard of the team’s performance makes us optimistic for the rest of the season,” Victor told Fox Sports.
“We had two lapses in concentration and that cost us qualification,” he said.
In the first leg, Atletico conceded a goal in the third minute of added time.
The result leaves only Nacional and Brazil’s Cruzeiro as former champions in the last eight.
Nacional now face Uruguay’s Defensor Sporting in the quarter-finals, playing away in Montevideo in the first leg, while Cruzeiro are up against Argentine champions San Lorenzo.
(Reporting by Rex Gowar in Buenos Aires; Editing by Peter Rutherford)
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