Diego Simeone's men were beaten 2-1 at the Allianz Arena by Bayern Munich, but qualified on away goals rule, after they won 1-0 at the Vincente Calderon last week.
Xabi Alonso's free-kick was deflected in, as Bayern levelled the tie on aggregate. Thomas Muller failed to give his side the advantage from the spot, as the excellent Jan Oblak pushed away his penalty.
Fernando Torres fed the sprinting Antoine Griezmann and he made no mistakes when one on one with Manuel Neuer to make it 1-1. Robert Lewandowski headed it to make it 2-1 and Torres also saw his penalty saved, as Bayern bowed out in the final four again.
Atletico will now face with city rivals Real Madrid or Manchester City in Milan.
