Wigan, based near Manchester, put together its roster for less than $30 million, while City's cost more than 10 times than amount.
But the season still could end on a low for Wigan, which is 18th in the Premier League at 9-19-8 with two games left. Wigan faces relegation to the second-tier League Championship next season unless it can climb in the standings.
"It's unbelievable. It's some achievement for everyone in the club," Wigan midfielder James McCarthy said. "Now it's down to the league. It's a massive week for the club. We have to put on a massive show for the rest of the season."
Wigan was led out onto the field by chairman Dave Whelan, whose playing career ended at old Wembley stadium when he broke a leg while playing for Blackburn in the 1960 final.
"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."
For City, the loss could intensify the turmoil threatening to engulf the club as it wasted the last chance to end the season with a trophy. The team has not denied a report that Malaga's Manuel Pellegrini has been approached to replace Roberto Mancini as manager.
Mancini helped end a 35-year trophy drought when City won the 2011 FA Cup, and the club won the Premier League last year.
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.
Wigan became the second history-maker this season at Wembley. Swansea won its first major trophy when it beat Bradford in the League Cup final in February.
Zabaleta became just the third player ejected from an FA Cup final when he was shown a second yellow card for fouling Callum McManaman. Manchester United's Kevin Moran was given a red card for fouling Everton's Peter Reid in 1985, and Arsenal's Jose Antonio Reyes received two yellow cards in 2005.