Ben Watson headed in the winner in the 90th minute at Wembley Stadium from Shaun Maloney\'s corner.
London: As blue-and-white confetti exploded under the Wembley arch, Wigan players lifted a trophy for the first time in the club's 81-year history.
In one of the biggest FA Cup final upsets, a team playing non-league football 35 years ago and assembled for barely $30 million beat big-spending Manchester City 1-0 on Saturday.
Winning English football's showpiece match was not only a reward for Wigan owner Dave Whelan's investment in the small northern club, but completed his unfinished business from the 1960 final.
After breaking a leg playing for Blackburn at the old Wembley, Whelan's career ended at the age of 23 and he started amassing the wealth that enabled him to ultimately finance Wigan.
"The dream has come true," Whelan said. "I'm repaid for 1960 when I broke my leg and we lost the match."
The game was drifting into extra time - and City defender Pablo Zabaleta had just been sent off - when substitute Ben Watson planted a header from Shaun Maloney's corner into the net in the 90th minute.
Watson had only just returned to action after recovering from a leg-break. "It's been a long six months for myself and it's been a dream - coming on in an FA Cup final and scoring the winner," Watson said.
But there was no champagne for the Wigan players after the match.
Now the history-makers will try to avoid the dubious distinction of being the first FA Cup winners to be relegated in the same season.
Wigan is in the drop zone with just two rounds remaining, three points from safety.
"We've got two massive games now to stay in the league and if we perform like that we'll be all right," Watson said. "We crack on again tomorrow."
Wigan is the second history-maker this season at Wembley, with Swansea winning its first major trophy in the League Cup final in February.
"Today it was David and Goliath," Wigan manager Roberto Martinez said. "It was following a dream ... we saw the underdogs play with incredible bravery, incredible belief and they defied the odds again. That's the FA Cup."
But the result throws into doubt the future of both managers.
Martinez, already widely admired in management thanks to his team's impressive performances, will be in demand even more - especially with Everton looking to replace Manchester United-bound David Moyes.
Martinez sidestepped questions on his future, focusing instead on the feat achieved by a team heading into the Europa League next season.
"Wigan Athletic is an incredible story," Martinez said. "Paul (Jewell) started everything, getting the team promoted to the Premier League. Now it's eight seasons and now we need to make sure the ninth season is round the corner, because we need to use European football in our favor.
"I mean, it doesn't matter who the manager is, there's a bigger picture than that."
At City, Roberto Mancini's future in the dugout is also looking uncertain with Spanish media reporting that Malaga's Manuel Pellegrini has been approached to replace the Italian.
City fans made their feeling clear toward the club's Abu Dhabi hierarchy, chanting in support of Mancini from the start and bellowing abuse about Pellegrini.
But there has been silence from City about Mancini's future.
As Mancini was questioned at Wembley about the apparent Pellegrini approach, City's media chief interjected to say "reportedly" but wouldn't deny the report when pushed to do so.
"I don't know why the club didn't stop this," Mancini said in a pointed about on the City hierarchy.
"If it's true we will see in the next two weeks ... if it's true, I'm stupid because I didn't understand anything about this," he added.
City is ending the season without a major trophy despite having the most expensively assembled squad in England, with more than $1 billion invested by Sheikh Mansour bin Zayed bin Sultan Al Nahyan since 2008.
The FA Cup enabled City to end its 35-year trophy drought two years ago, but despite going on to win the Premier League last season, the club has appeared to go backwards in this campaign.
The Premier League trophy was conceded to Manchester United with four games to go, while City exited the Champions League in the group stage for the second successive season.
And on Saturday, City was outshone by Wigan.
Belying their lowly position in the Premier League, the Wigan players started with confidence, looking assured on the ball.
The finishing lacked venom, though, until the end - even though the team created chances from the start.
Arouna Kone burst forward after nine minutes and sent the ball forward to Callum McManaman, who miscued his shot and missed the target.
The closest City came in the first half was Joel Robles sliding out to block Carlos Tevez's shot.
McManaman, who caused City defender Gael Clichy trouble throughout down the right flank, worked his way into the penalty area again before halftime, forced Joe Hart off his line and found the space to shoot, but was denied by Zabaleta's block.
In a second half lacking clear-cut chances, Joel blocked a header from City substitute Jack Rodwell, and Maloney hit the top of the crossbar.
Wigan's breakthrough came after Zabaleta became just the third player to get sent off in an FA Cup final, when he was shown a second yellow card for bringing down McManaman.