The joy of Atletico's first penalty shootout triumph in Europe will diminish once the dust settles on a narrow victory that did little to suggest they had rediscovered a cutting edge up front.
Midfielder Mario Suarez's first half effort was the only goal either team could muster at the Calderon, his goal levelling up the tie after Diego Simeone's side had lost 1-0 away in Germany.
It was a scrappy match in which Leverkusen failed to take several chances of their own before Suarez's decisive intervention.
Atletico improved as they game progressed but only managed to put the visitors under any sustained pressure towards the end of normal time.
Mario Mandzukic was restored to the starting lineup, having been relegated to the bench for two games as well as missing the 0-0 draw with Espanyol in La Liga last weekend through suspension.
However, he failed to provide the solution for a faltering Atletico attack that has now scored just two goals in the last five games in all competitions.
The run has also seen the La Liga champions drop down to fourth place in the domestic standings.
Fernando Torres replaced Mandzukic after 82 minutes as Simeone's side looked for a winning goal but the Spanish striker was unable to prevent the tie from going to penalties.
"In the Champions League it is very difficult and the Last 16 is not as easy as people think," Torres told reporters.
"We controlled the game but we did not find it easy to score. Then in the penalties, it is down to the team with the most luck." Torres scored Atletico's fifth penalty and it was a special night for the homegrown talent. After spells at Liverpool and Chelsea, he moved to AC Milan and is currently on-loan at his boyhood club from the Italian outfit.
"I was looking forward to experience matches like this at the Calderon," he said. "It was incredible and I only have words of thanks to the fans who backed us right to the end. There is no doubt that I made the right decision to come back here."
(Editing by John O'Brien)
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