And it shattered the hopes of favorite Barcelona, which had reached the semifinals seven times in the last eight seasons.
Atletico Madrid left the Camp Nou infuriated with the refereeing last week after its striker Fernando Torres was sent off in the 35th minute. On Wednesday, it was Barcelona that had reason to complain after a hand ball by Gabi Fernandez that appeared to be inside the area - but was judged by the referee outside the box in second-half injury time.
Lionel Messi's ensuing free kick sailed over the crossbar in his team's last chance.
Only twice Barcelona had failed to advance after winning the first leg in its previous 40 attempts in UEFA competitions.