Leverkusen won last month's first leg in Germany 1-0 and a goal from Atletico midfielder Mario Suarez in the 27th minute of a finely-balanced and absorbing return match left the teams locked at 1-1 after extra time.
Both sides failed with two penalties before visiting striker Stefan Kiessling fired his side's fifth spot kick over the crossbar to give the hosts a 3-2 shootout victory and send the fans thronging the Calderon into ecstasy.
It was Atletico's first shootout triumph in four attempts in European competition and earned them a place in Friday's quarter-final draw.
"What defines us is that we are a team," said Suarez who also netted a penalty in the shootout.
"We don't care who we get in the next round," he told Spanish television. "It will be one of the best and nobody will want to play us."
Roared on by the home support, Diego Simeone’s men came storming out of the blocks but Leverkusen refused to be intimidated and Suarez's deflected effort that went in off defender Omer Toprak was their first shot. It was more of the same in the second half with a fired-up Atletico pressing forward without really threatening and a well-organised Leverkusen looking to hit back on the counter attack. Atletico playmaker Arda Turan fired over with a volley on the run in the 69th minute after good work down the left from Antoine Griezmann and a Koke free kick evaded everyone and almost sneaked inside the post a minute later. The players clearly tired and chances were scarce in extra time. Atletico midfielder Raul Garcia had the clearest in the 106th minute when he blasted an angled shot straight at keeper Bernd Leno while Leverkusen captain Simon Rolfes lashed a long-range effort just wide in the 111th.
The shootout started badly for Atletico when Garcia fired over the bar but Jan Oblak then saved from Hakan Calhanoglu before Griezmann, Rolfes and Suarez all scored.
Toprak blazed over and Koke's was brilliantly saved by Leno before substitute Fernando Torres made it 3-2 with the fifth spot kick for Atletico who lost to Real Madrid in last year's final.
(Editing by Tony Jimenez)
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