Title holder Bayern Munich came alive in the second half after falling behind and beat Manchester United 3-1 on Wednesday to advance to its third straight Champions League semifinal.
Bayern advanced 4-2 on aggregate after a 1-1 draw in Manchester.
Bayern dominated the first half but failed to make much out of its possession advantage, and Patrice Evra put United ahead with a superb volley in the 57th minute.
The lead lasted only two minutes before Mario Mandzukic got the equalizer. Thomas Mueller made it 2-1 in the 68th and Arjen Robben secured the victory in the 76th.
"I think it's great how we came back despite this little setback," Mueller said. "If we look at both matches, I think we deserved to come through."
The loss means United looks set to miss the Champions League next season for the first time since 1995-96. David Moyes' team is only seventh in the Premier League, with only the faintest of hopes of finishing in the top four. Its only realistic chance of qualifying for Europe's top competition was to win it this season, but now the team's last chance for a trophy is also gone.
We concentrated so fabulously but to give up that goal at that moment was very disappointing," Moyes said.
United spent much of the game defending and waiting for counterattacks and that was not enough to eliminate the defending champion.
Koke guides Atletico past Barcelona
Koke's early goal guided Atletico Madrid to a 1-0 win against Barcelona and into the Champions League semifinals with a 2-1 aggregate victory.
Adrian Lopez filled in for injured striker Diego Costa and created the fifth-minute opener after finding the post, as the Atletico forward headed an ensuing cross on to Koke to fire home.
The boisterous atmosphere at the Vicente Calderon Stadium unsettled Barcelona early on, and Atletico striker David Villa hit the woodwork twice within the opening 20 minutes.
Barcelona dug in but produced few tangible scoring chances apart from a pair of first-half misses by Lionel Messi.
Atletico, which leads Barcelona by one point in the Spanish league, reached the last four of Europe's top competition for the first time since 1974.
"We just have to keep working hard and stay calm because we still haven't won anything," said Atletico coach Diego Simeone, whose team will face either crosstown rival Real Madrid, Chelsea, or Bayern Munich in a two-legged semifinal.
The teams had played four previous games this season which all ended in draws, but Atletico's breakthrough kept Barcelona from the semifinals for the first time in seven seasons.
"There was a big difference between one team and another early on. We couldn't string together four or five passes like we needed to," Barcelona coach Gerardo Martino said. "If we had managed to equalize we might have been able to play the game we wanted."
"I thought we deserved the draw," Barcelona midfielder Xavi Hernandez said, despite his team managing just five attempts on goal to Atletico's nine. "The game got away from us."