It was a goal that had all the hallmarks of City's slick attacking play, which was missing from the visitors for most of the match. Pep Guardiola's team still found a way back into the game in the 69th minute when Aguero had a shot blocked before playing the ball out to Bernardo Silva, who rifled a shot with the outside of his boot into the corner.
City continued to pressure Swansea and the penalty came when Cameron Carter-Vickers was adjudged to have fouled Raheem Sterling in the box, even though replays clearly showed he got the ball.
Aguero's spot kick hit the post before the ball went in off luckless goalkeeper Kristoffer Nordfeldt.
The Argentina striker then headed the winner in the 88th minute but replays showed he was offside when the cross was delivered, highlighting the absence of video reviews for the game. VAR was in use only at Premier League stadiums in the quarter-finals.
"If it's not a penalty, I'm sorry. If it's offside, I'm sorry," said Guardiola, who added he had not seen replays of either incident. "Why is VAR not here? That's the question for the authorities."
Swansea manager Graham Potter refused to blame the referee.
"City had chances of course, you can't deny if you look at the game that they deserved to win," Potter said. "But for the players, it's disappointing to lose goals in that manner. That's life, referees make mistakes as well."
Wolves, meanwhile, reached the semifinals for the first time since 1998 after Raul Jimenez and Diego Jota scored in a six-minute span in the second half.
Jimenez swivelled in the box and fired a shot past two defenders and goalkeeper Sergio Romero, who had made a string of saves to keep United in the game.
Jota then finished off a lightning counter-attack to double the lead, which never looked under threat until Marcus Rashford pulled back a consolation goal deep into injury time.
United had knocked out Arsenal and Chelsea in the previous two rounds but manager Ole Gunnar Solskjaer now has only the Champions League left as a trophy target, although his team has to get past Barcelona in the last eight.
Watford also reached the last four after substitute Andre Gray scored two minutes after coming off the bench to secure a 2-1 victory over Crystal Palace.
Millwall hosted Brighton in the last quarter-final overnight.
In the Premier League, Huddersfield's hopes of staving off Premier League relegation are all but over after giving up a two-goal lead to lose 4-3 at West Ham, while Burnley put themselves in danger of going down when they couldn't convert a one-man advantage against Leicester City, losing 2-1 after conceding a last-minute goal. In the other game, Newcastle drew 2-2 at Bournemouth.
- AP
