Pep Guardiola’s Bayern Munich lost their third consecutive UEFA Champions League semi-final against Spanish opposition.
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Bayern needed a two-goal margin win to advance break the Spanish curse which had seen them eliminated at this stage by Real Madrid and Barcelona in 2014 and 2015 respectively.
Xabi Alonso opened the scoring for the Germans with a deflected free-kick in the 30th minute only to see his team-mate Thomas Muller miss with a penalty a couple of minutes later.
Antoine Griezmann got Atletico back in control of the tie with a 54th minute equaliser.
Bayern went ahead again in the 74th minute through Robert Lewandowski's strike.
Fernando Torres later in the game missed a penalty, to leave Bayern over five minutes in which to grab the goal they needed.
But they could not breach Atletico's defence leaving the Spaniards to qualify for the May 28 final at San Siro on the away goal rule after the tie ended 2-2 on aggregate.