City, newly crowned League Cup champions, were bidding to avenge their 1-0 defeat in last season’s final, but instead it was the holders — managed by former City striker Uwe Rosler — who advanced to a last-four date with Arsenal.
Jordi Gomez gave Wigan the lead with a 27th-minute penalty after Martin Demichelis fouled Marc Antoine-Fortune and James Perch made it 2-0 within seconds of kick-off in the second half.
Samir Nasri pulled a goal back for City with 22 minutes remaining, but the Championship side — relegated within days of last season’s final — withstood heavy pressure from the hosts to record another famous FA Cup win.
The Etihad was buoyant after City’s 3-1 win over Sunderland in last weekend’s League Cup final, but the home fans were silenced in the 27th minute when Wigan took the lead.
A neat turn took Fortune past Demichelis on the Wigan left and after the Argentine brought him down, Gomez sent goalkeeper Costel Pantilimon the wrong way from the penalty spot.
City’s frustration was evident, with Nasri booked for kicking the ball away, and Wigan extended their lead early in the second half when Perch stole in front of Gael Clichy to tuck in a low cross from James McArthur.
City manager Manuel Pellegrini reacted by sending on James Milner, David Silva and Edin Dzeko, and the latter came within a whisker of equalising in the 64th minute with a header that hit the post.
The hosts continued to push, though, and four minutes later Nasri dragged them back into the tie with a left-foot shot from outside the box that skidded into the bottom-right corner.
City threw everything at Wigan in the closing stages, with Emmerson Boyce producing an extraordinary goal-line block to thwart Dzeko, but Wigan held on by the skin of their teeth.
– Hull, Sheffield United advance
Earlier, Hull City and giant-killers Sheffield United set up an unlikely semi-final showdown after coming through their respective quarter-final ties.
Hull defeated Premier League rivals Sunderland 3-0 at the KC Stadium to reach the last four for the first time since 1930, while third-tier United overcame Charlton Athletic.
Hull’s Sone Aluko saw a first-half penalty saved by Sunderland goalkeeper Oscar Ustari, but three goals in nine minutes from Curtis Davies, David Meyler and Matty Fryatt in the second period gave the hosts victory.
“I’ve just seen the draw and it’s a great one,” said Hull manager Steve Bruce, who twice won the trophy as a player with Manchester United.
“Sheffield United have had a wonderful run and beaten every team put in front of them.
“But you have got to be honest — you want to avoid the big boys and I’m sure Sheffield United will be thinking the same having drawn us.”
Sheffield United continued their remarkable journey in the FA Cup by upsetting second-tier Charlton 2-0 at Bramall Lane.
Managed by Nigel Clough, son of legendary former Nottingham Forest manager Brian, the Blades became the first team from the third tier to reach the last four since Wycombe Wanderers in 2001.
“I’m just delighted for everybody that we’re going to Wembley, especially the players,” Clough, whose late father never won the tournament, told BT Sport.
“To win nine games on the spin, they deserve an immense amount of credit. We hope to play a lot more big games like this in the future.”
Having previously accounted for Premier League sides Fulham and Aston Villa, as well as second-tier Forest, the Blades prevailed thanks to quick-fire goals from Ryan Flynn and John Brayford mid-way through the second half.