City's Wembley dream turned into a nightmare as Wigan substitute Ben Watson grabbed a late, late winner to stun Roberto Mancini's men.
The Blues rarely got to grips with their tenth FA Cup Final and finished with ten men as Pablo Zabaleta was sent off for a second yellow card seven minutes from time.
Mancini was chasing his third trophy in as many seasons - and City's second FA Cup in three years - but too many of his players failed to reproduce the form that swept them through earlier rounds.
The teams are separated by 16 places and 40 points in the Premier League, but City found themselves on the wrong end of the biggest Final upset since Wimbledon beat Liverpool in 1988.
Mancini began the day by handing City fans a bit of a shock - not to mention Romanian goalkeeper Costel Pantilimon. The No2 had played in every round, keeping an impressive clean sheet until the semi-final against Chelsea.
However, it was Joe Hart who got the nod from the manager, leaving Pantilimon on the bench.
It put the England goalkeeper in the FA Cup firing line for the first time since City beat Stoke 1-0 in the Final two years ago.
Hart was one of only three players to keep their place from the line-up that beat West Brom in midweek - Carlos Tevez and Samir Nasri were the others - in what was arguably the strongest side Mancini had at his disposal.
Not that Wigan were overawed by the array of talent ranged before them - they certainly didn't play like a team facing the severe threat of relegation.
It might have been different had Yaya Toure's right-footed curler after three minutes found the target rather than Joel's parrying fists. Instead Wigan proceeded to match City in a first half that frustrated the Blues.
There were key interventions by Matija Nastasic, whose block on A Shaun Maloney shot raised too-hopeful penalty appeals, and by Gareth Barry, whose tackle stopped James McArthur in his tracks as he homed in on goal.
When City did piece together a rare moment of their flowing style - Nasri to Sergio Aguero to Carlos Tevez - the Argentine striker's shot was saved by a foot as the Wigan keeper went the other way just before the half-hour.
But the drama was by no means confined to that end. Pablo Zabaleta, one of City's better performers before his early exit, made a saving challenge on Roger Espinoza that had some - but not referee Marriner - crying "penalty". TV replays backed his judgement.
Then within a minute danger man McManaman executed a remarkable run that took him into the penalty area and around Hart but back away from goal, with his final shot blocked by scrambling defender Zabaleta.
The Blues got the message when Mancini urged them from the touchline to sharpen up, and Silva, with a glancing header, then Barry, with a shot too close to the keeper, signalled that City were aiming to step up the tempo.
Aguero was close to breaking the deadlock when an outstretched leg just prevented him connecting with a Tevez cross, but as the game wore on so the frustration grew, especially when Zabaleta's inviting cross was too far away for Silva to pounce.
Aguero was not alone in feeling he was denied a penalty on 57 minutes when Paul Scharner fell full length and caught his ankle in the area, but Mr Marriner was unmoved, though he did book Zabaleta soon after for bringing down McManaman.
The Wigan youngster was the key to their attacking threat, and it needed a great block from Kompany to defy him when he shimmied into the penalty area on 65 minutes.
When Maloney managed to drop a free kick onto the top of Hart's bar after Nastasic saw yellow for fouling McManaman after 74 minutes, the alarm bells were ringing for City.
But the decibel count hit a new level with 83 minutes gone when Zabaleta brought down McManaman for a second time, after Barry gave away the ball, and saw yellow then red cards.
Wigan sensed their time had come, and from a Maloney corner right on 90 minutes substitute Watson stole in front of Rodwell and headed beyond Hart to silence City's stunned following.