Having won the first leg 1-0 in Spain,
Atletico advanced thanks to Antoine Griezmann's crucial away goal in
Munich as the tie finished 2-2 on aggregate.
Xabi Alonso and Robert Lewandowski netted for
Bayern on a night when both teams missed penalties as Atletico secured a
spot in the final in Milan on May 28, where they will face either Real
Madrid or Manchester City.
Bayern and Guardiola will rue Thomas Mueller's
saved first-half penalty just after Alonso had given the hosts the lead
by crashing home his free-kick.
There was similar drama in the second half when Manuel Neuer saved Fernando Torres' late penalty attempt for Atletico.
After Griezmann put Atletico level in the
second half, Lewandowski gave Bayern brief hope when he headed home, but
the Bundesliga leaders could not find the crucial third goal they
needed.
Simeone's Atletico, level on points with
Barcelona at the top of La Liga with two games of the campaign left,
face a busy few weeks as they prepare for their second Champions league
final in three seasons.
Meanwhile, with their dreams of a treble over, Bayern are left to focus on winning a domestic double in Guardiola's swansong.
Bayern can become the first club to win four
consecutive German league titles if they win at Ingolstadt on Saturday
and they also face Borussia Dortmund in the German Cup final in Berlin
on May 21.
However, their European exit will be a bitter
pill to swallow for Bayern after they lost the 2014 semi-final to Real
Madrid 5-0 on aggregate and exited at the same stage in 2015 with a 5-3
aggregate defeat to Barcelona.
Having been hammered in the German media for
starting the Madrid leg without Mueller, Guardiola included the Germany
star and also brought in Jerome Boateng and Franck Ribery for the
return.
Simeone made just one change from the first
leg with centre-back Diego Godin returning in place of Stefan Savic
after recovering from a hamstring injury.
PENALTY MISSES
Atletico arrived in Munich having won their
previous seven games and had not conceded a goal in their previous six.
However, the latter run was broken when Alonso drilled his free-kick
into the net in the 31st minute to level the tie on aggregate.
His shot took a slight deflection off Jose
Maria Gimenez to wrong-foot Atletico goalkeeper Jan Oblak, and Bayern
could have made it 2-0 on the night just three minutes later.
Gimenez was booked for conceding a penalty
when he pulled down Javi Martinez in the area, but Oblak saved Mueller's
weak effort from 12 yards.
Simeone replaced Augusto Fernandez with
Yannick Carrasco at the break and moved Griezmann out wide, and the
tactical switch paid dividends as the visitors struck nine minutes into
the second period from their first clear chance of the game.
Torres sent Griezmann clear in behind the Bayern defence and the France striker kept his cool before firing past Neuer.
Bayern were left needing to score twice and
they got one back when David Alaba's cross was headed back across the
six-yard box by Arturo Vidal and Lewandowski nodded home his ninth
Champions League goal of the season on 74 minutes.
Neuer came to Bayern's rescue by saving
Torres' penalty attempt in the dying stages after the striker was
brought down by Martinez, but it could not save Bayern from bowing out.
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