Friday's draw in Nyon not only paired powerhouses Bayern and Real together but also kept alive the intriguing possibility of an all-Madrid final in Lisbon next month.
The draw also puts Atletico's goalkeeper Thibaut Courtois up against his parent club Chelsea after UEFA said in a statement on Friday that the on-loan Belgian is eligible to play against the Londoners.
Atletico and Real will be at home in the first legs taking place on April 22-23 with the second legs the week after.
Real have not won the competition since 2002 and will have to end Bayern's hopes of becoming the first back-to-back winners, if they are to stay on course.
They will also be wary of a poor record against Bayern Munich in the competition, losing to the Bavarian club in four of the five semi-finals they have contested.
"What can I say? Bayern is an extraordinary organisation, one of the most prestigious teams in the world and the current champion," Real director Emilio Butragueno said.
"They have an extraordinary team both collectively and individually and without doubt they will be an extraordinary opponent for us.
"But it's the fourth semi-finals in a row for us and we are hopeful of making the final."
They will be sweating on the fitness of Cristiano Ronaldo after the Portugese forward's knee injury prevented him playing in the second leg of the quarter-final against Borussia Dortmund this week - a match Real lost 2-0.
"We have to wait and see how he develops," Butragueno said.
"Obviously he and the doctors will do everything to make sure he is back as soon as possible."
Bayern's chairman Karl-Heinz Rummenigge said a meeting with Real would be "incredibly tough".
"All Bayern and Real fans can justifiably look forward to a fantastic clash," he told the club's website.
"We've been drawn to play one of the best clubs in the world and they're a fantastic team."
Surprise Spanish league leaders Atletico, who knocked out Barcelona this week, are the only one of the last four not to have won Europe's elite club competition but crushed then European champions Chelsea 4-1 in the Super Cup final in 2012.
Chelsea, for whom manager Jose Mourinho is seeking to win it with a third different club having triumphed with Porto and Inter Milan, are in the semis for the seventh time in 11 years.
Chelsea chief executive Ron Gourlay played down any controversy surrounding Courtois's availability for the tie, although did not comment on reports that a clause in the agreement between the clubs means Atletico will have to pay up to 5 million pounds if he plays in both legs.
"The loan was arranged back at the start of the season and it's quite simple, Thibaut can play against Chelsea. That was never in doubt," he told Sky Sports.
While Chelsea will possibly be relieved to have avoided Bayern and Real Madrid, Diego Simeone's Atletico side represent a formidable obstacle.
"We are very happy to be here together with three such magnificent teams," sporting director Jose Luis Perez Caminero said following the draw.
"I think it will be a balanced tie. (Chelsea) have a great team and great individual players.
"We will try to be as effective as possible with our style of play and try to reach the final, a dream not only for the players and the club but for all the fans."
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