With speculation swirling about the future of manager Erik ten Hag, United ripped up the form book as first-half goals from teenagers Alejandro Garnacho and Kobbie Mainoo proved enough for them to lift the trophy for a 13th time.
They had to endure a second-half siege, however, as City swarmed forward and a late goal by Jeremy Doku set up a nerve-shredding finale before United could celebrate their first FA Cup final triumph for eight years.
Premier League champions City, bidding to become the first club to win the double in successive seasons, had been on a 35-match unbeaten run in all competitions in open play.
But a week after sealing an unprecedented fourth successive Premier League crown, Pep Guardiola's side were well below their best, gifting Garnacho a 30th-minute opener before fellow 19-year-old Mainoo made it 2-0.
United stood firm, however, to seal the best result of Ten Hag's two-season reign and qualification for next season's Europa League, although it is highly likely the Dutchman will not be in charge next season.
"Incredible. Nobody believed in us. But we're a team, all together. We fought, the game of our lives," Garnacho, who became the first Argentine to score in the Cup final since Ricky Villa for Tottenham Hotspur against City in 1981, said.
The build-up had been dominated by talk of the chasm between the two Manchester clubs with City having won the title for the sixth time in eight years under Guardiola and United suffering their worst Premier League campaign, finishing eighth.
FUTURE DOUBT
Ten Hag's future was also clouded in uncertainty with reports that the showpiece would be his last game in charge, whatever the outcome.
But he could smile at the end as he led his players up the Wembley steps with his name being sung by United's ecstatic fans who a few hours earlier may have been fearing a drubbing.
"The performance was very good against the best team in the world," Ten Hag told the BBC. "We've had so many setbacks this season with all the injuries but we showed so much resilience and I'm proud of them."
Asked whether it was his last game, the former Ajax Amsterdam coach said: "I don't know. For me this is a project and when I came in it was a mess."
Garnacho, one of the few positives in United's season, had the game's first shot on target and his movement was a constant threat to a City defence featuring two changes with John Stones and Nathan Ake handed starts.
United's 30th-minute opener was a shocker for City. A long ball forward should have been meat and drink for Josko Gvardiol but his headed back pass went over advancing keeper Stefan Ortega and Garnacho accepted the unexpected gift with glee.
Marcus Rashford had a goal ruled out minutes later with Garnacho adjudged offside but it was not long before United were in dreamland.
This time there was no help required as a slick move saw Garnacho play the ball in to captain Bruno Fernandes whose superb no-look pass released Mainoo to slot past Ortega.
City were stung but substitute Doku sparked them into life. Haaland smashed a shot against the crossbar and United keeper Andre Onana made a superb save to keep out a Kyle Walker effort while Julian Alvarez, who came on for Kevin De Bruyne, fired a shot over the crossbar.
Alvarez side-footed wide from in front of goal but United's rearguard, led by the superb Lisandro Martinez whose injury-absences this season have compromised United's back four, held firm.
City finally broke through with Doku whipping a shot past Onana at his near post but they had left it too late.
