Jordi Gomez and James Perch scored in either half to continue Wigan's love-affair with this competition and although Samir Nasri reduced the deficit, the Latics defence held firm to send the Sky Bet Championship club back to Wembley for a semi-final showdown with Arsenal.
City now head to Barcelona in the Champions League hoping to overturn a two-goal deficit and facing the very-real prospect of being eliminated from two competitions in the space of four days.
"I think it's the worst first half we've had in the year because we didn't have the pace to play against a team that is in a good moment," said boss Manuel Pellegrini.
"They won five games in a row so we knew before the match we are going to play a difficult team, maybe we thought that was not going to be so difficult and when we react it was too late."
Wigan's disciplined formation saw a bank of four stifle any space in front of their back three which left the likes of Nasri, usually so efficient between the lines, frustrated, which the Frenchman showcased when he was booked for kicking the ball away in anger.
Pellegrini, though, was adamant the FA Cup holders had not stunned him and his players with the way they approached the contest.
"We knew exactly how Wigan play; it's not a tactical problem, it was a pace problem, a tempo problem," the Chilean added.
"In the last 35 minutes they continue playing the same way and we continue playing the same way. We had at least three of four chances to score more goals. When you don't have the same intensity it's very difficult to win."
- Sports & Recreation
- Samir Nasri
- Jordi Gomez