Not many favoured Leverkusen to advance but after their first leg 1-0 win in Germany courtesy of Hakan Calhanoglu's goal, hopes of finally ending their losing run in the round of 16 were ignited.
Roger Schmidt's team have been playing a good season in the Bundesliga, sitting in fourth place with their exciting brand of quick, counter-attacking football with the addition of Calhanoglu and Karim Bellarabi this season.
The Spanish champions, losing finalists last season, were in no way spectacular in the first leg and were on the backfoot again on Tuesday until they scored following some sloppy defending midway through the first half.
But Leverkusen failed to make possession count and then missed three penalties in the shootout after the game ended 1-0 after extra time.
Their opponents were equally bad from the spot, missing two penalties themselves before striker Stefan Kiessling sent a wild effort over the crossbar with the Bundesliga side's fifth penalty to send Atletico through.
"We were not courageous enough," said Leverkusen defender Gonzalo Castro. "You could see that some of us were very sad and lost in their thoughts. But we worked hard before we let in a stupid goal that should normally not happen."
Indicative of their lack of mental strength was the weak penalty taken by Calhanoglu, by far the best Leverkusen player this season and a hugely talented midfielder.
The 21-year-old Turkey international simply rolled the ball into the hands of keeper Jan Oblak, choking at the worst possible moment this season and crushing Leverkusen's dream of a successful European run after more than a decade.
"Obviously being eliminated on penalties has a bit to do with nerves," said coach Schmidt. "It would have been easier taking penalties in our own stadium."
"The fans' noise maybe made my players a bit more nervous. Hakan should write off his penalty because the team put up a great fight."
With Bayern Munich awaiting in the German Cup quarter-finals and Schalke 04 in the league on Saturday, Leverkusen have enough big games ahead to make amends for their European exit.
(Editing by Sudipto Ganguly)
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