Alex Nimely gave City a dream start when he scored after 15 minutes but United hit back with goals from Davide Petrucci and Jesse Lingard on either side of half-time to lift the cup.
City were looking to end a 39-year wait for success in the competition at Leyland’s County Ground, having last won the title in 1973/74 with a win over Morecambe.
More familiar opposition stood in the way of the trophy this time in the form of City’s neighbours, meeting the Blues in the final for the first time in the competition’s 134 year history.
With members of Patrick Vieira’s EDS side only returning from the u19 competition in Oberndorf on Monday evening, the XI was a mixture of younger under-18s and those too old for the competition in Germany.
That meant that Kieran Kennedy and Harry Bunn were able to resume their injury comebacks from lay-offs which blighted their 2012/13 campaigns.
There was also room in the squad for England youth international right-back Ashley Smith-Brown and Jack Byrne who both trained with Manuel Pellegrini’s first-team this week, and a place in the line-up for Wales u21 international Emyr Huws, who captained the team.
Head of Academy Coaching Scott Sellars and under-18s boss Jason Wilcox took the team, while Vieira watched on from the stands on a glorious mid-summer’s evening at Lancashire FA HQ.
City got off to a flying start and could have been a goal up in the opening minute after a precise cross-field pass by Huws was taken down by Bunn who swivelled and fired his shot just a yard past the far post.
The match had the feeling of a pre-season curtain raiser, with a carpet-like surface playing host to attractive, attacking football from both sides but the team in blue were making all the in-roads in the opening exchanges and enjoyed a flurry of good chances to take the lead.
Most of City’s joy was coming from the right hand side, with Adam Drury and Bunn linking up to fine effect but the team-wide pressing of the opposition was also a factor in this bright start, forcing mistakes from a United team who were left without a second to settle on the ball.
This incessant pressure was rewarded after 15 minutes when Louis Hutton’s blocked shot fell into the path of Alex Nimely who blasted his shot from close range into the roof of the net to give City the lead.
United’s best chance of notching looked like coming from a set piece and they nearly had one when Federico Macheda was felled in the box by Eirik Johansen but the referee deemed that the Norwegian played the ball as he rushed out to close down.
From this point on, City’s opponents seemed to grow in confidence and the Blues’ pressing lost some of its’ intensity so there was a feeling of inevitability in the air when Davide Petrucci angled a shot around Johansen into the top corner to level the scores on the half-hour mark.
City did manage to steady the ship in the final minutes of the first period, putting their foot on the ball to build up from the back and maintain parity with comfort until the half-time whistle.
This impressive end to the half carried over into the second period and Nimely had the chance to double his tally after a lightning fast counter-attack spearheaded by Bunn down the right.
The former Oldham loanee found Nimely in the centre of the penalty area with the goalkeeper to beat but the ball hit the crossbar and went behind.
It was a less open half that the dramatic first but City were so close to re-taking the lead with 20 minutes to play after Huws fed Bunn but his shot was headed off the line.
City were made to pay for not taking one of their many chances after United were awarded a debatable penalty for an adjudged trip by Smith-Brown.
Jesse Lingard picked himself up to convert past Johansen, meaning the Blues were trailing with just 15 minutes to play.
Wilcox and Sellars threw on Devante Cole to try and find an equaliser with ten minutes to go but City’s neighbours held out to lift the first trophy of the season.
City EDS begin their Barclays u21 Premier League campaign at home to Fulham on Sunday afternoon.
Kick-off at Hyde FC is at 1pm.