City captain Gundogan scored the fastest goal in FA Cup final history with a stunning volley after 12 seconds and struck what proved to be the winner seven minutes after halftime.
In doing so the 32-year-old, who is expected to leave City in the summer after seven trophy-laden years, became the oldest player to score an FA Cup final brace since Nat Lofthouse for Bolton Wanderers in 1958, also against United.
United, seeking to win both domestic cups in the same season for the first time in their history and wreck City's hopes of emulating their own historic 1999 treble, had levelled with a 33rd-minute Bruno Fernandes penalty.
Pep Guardiola's side resisted some late United pressure to win the trophy for a seventh time.
It is the 13th time the English league and FA Cup double has been achieved. But City now want more and travel to Istanbul to face Inter Milan seeking to be crowned European champions for the first time and to equal United's 1998-99 Premier League/FA Cup/Champions League sweep under Alex Ferguson.
"Now we can talk about the treble," Guardiola, who has won 11 trophies since arriving at City in 2016, said.
"Of course we still have to win the Champions League. We performed so well for our city and our fans. It was so important for us today. The FA Cup is so nice."
For the first time in 190 meetings the clubs were clashing for silverware, and not just bragging rights, and Wembley was decked in red and sky blue as fans braved rail strikes to descend en masse on the capital.
Smoke from the pre-match pyrotechnics had not even cleared when City took the lead in spectacular fashion.
Keeper Stefan Ortega's long punt towards Erling Haaland and as the ball bounced into the path of Gundogan who did not hesitate to send a dipping right-foot volley arcing over a transfixed David de Gea.
"The ball just was placed amazingly for me and I just had to hit it," he said. "Obviously it was quite a good strike and it went in and it was amazing."
It eclipsed the previous fastest FA Cup final goal scored by Louis Saha after 25 seconds for Everton against Chelsea in 2009 and City threatened to run riot against a stunned United.
Rodri and Jack Grealish both failed to convert good chances in the opening five minutes in which United barely touched the ball while Haaland and Kevin de Bruyne also went close for City before United were handed an unexpected gift.
United right back Aaron Wan-Bissaka headed a diagonal ball harmlessly across the area and as play continued referee Paul Tierney was instructed to check a pitch-side VAR monitor for a possible handball by Grealish.
It was extremely harsh on Grealish, but Tierney pointed to the spot and Fernandes calmly shuffled up to send Ortega the wrong way with his penalty and spark celebrations at the east end of the stadium where United's fans were packed.
Briefly United looked City's match and Raphael Varane volleyed over from a corner as halftime approached.
But it proved an illusion. City needed slightly longer in the second half to re-establish their superiority and again it was Gundogan displaying his knack of scoring crucial goals.
This time he was picked out by De Bruyne's chipped pass and his left-foot volley, not struck anywhere near as perfectly as his earlier effort, bounced its way through a crowded area and crept inside De Gea's right-hand post.
Gundogan was denied a hat-trick by an offside flag and as the minutes ticked down City looked edgy with United substitute Alejandro Garnacho curling a shot agonisingly wide and a crazy goalmouth scramble in stoppage time ended with the ball bouncing off City's crossbar.
For United they can console themselves with a League Cup trophy in manager Erik Ten Hag's encouraging first season and will hope Inter can stop City next Saturday.