Jon Obika and Alex Pritchard both registered and at 2-0, there only looked one outcome.
But somehow the home team turned it around in the second half. Alarm bells started to ring when Marnick Vermijl made it 2-1 on 59 minutes and a double from Larnell Cole after 74 and 88 minutes completed the turnaround.
Naturally downcast after the final whistle, the players shouldn't let the result of the final overshadow what has been a fantastic campaign full of free-flowing football that reaped 17 wins from 28 matches and a goal tally of 82.
There was one change to last week's semi-final win against Everton as Harry Kane came in for Kevin Stewart.
Apart from a couple of half-chances, it was pretty much one-way traffic in the first half.
The first effort at goal came in the sixth minute as Tom Carroll curled just over from 25 yards.
Obika turned Kane's low cross onto the crossbar in the 18th minute to spark a rush of action at both ends.
Cole was next up, a sharp turn and shot wide, Cristian Ceballos then dipped a 25-yarder inches wide, Jesse Lingard showed quick feet to work an opening but miss the target again and finally, Kane unleashed a ripper from 25 yards that rattled the upright - all that in the space of three minutes.
We soon settled back into control and the opening goal arrived on 29 minutes.
Obika climbed with Ben Amos, who didn't deal with the high ball, Pritchard was first on the scene and headed towards goal and Obika was there to turn home from close range.
The first half display got the flourish it deserved with the second goal, a sweet strike from Pritchard that flew across Amos into the bottom corner from 25 yards.
It was a quiet start to the second half but United slowly clawed their way back into the game. Lingard pushed up to support Januzaj and the home team enjoyed a sustained spell of possession for the first time.
That led to a goal back and a fine strike from full-back Vermijl, who fired across Jordan Archer into the far corner on 59 minutes.
Kenny McEvoy joined the action for Pritchard on 64 minutes and was soon involved, a dart to the right byline and cross had Amos peddling backwards to tip over. Ceballos then tested the goalkeeper again from 22 yards.
United's equaliser arrived on 74 minutes. Lingard led a break and played in Januzaj down the left, he fired in a low cross that found Cole who turned inside Archer before firing into the roof of the net.
Play soon switched to the United end as Kane played in Obika, who clipped over Amos but wide of the target.
The next chance fell to McEvoy on 83 minutes as Kane dropped in a cross for Obika and the ball came out to the winger, who walked onto a full volley that flashed into the side-netting.
It could have gone either way at this point but momentum was with United and they clinched the trophy with two minutes left. Januzaj got down the right and cut the ball back to Cole, who controlled and fired into the bottom corner.
Manchester United (4-1-4-1): Amos; Vermijl, Thorpe, Keane, James; Ekangamene; Cole, Pearson (Lawrence, 56), Tinnicliffe, Lingard; Januzaj. Unused subs: Grimshaw, Sutherland, Pereira, Wilson.
Spurs (4-3-3): Archer; Fredericks, Hall, Veljkovic, Fryers; Bentaleb, Carroll, Pritchard (McEvoy, 64); Obika, Kane, Ceballos. Subs: Barthram, Miles, Gallifuoco, Stewart.
The lads produced the form that took them to both titles in the first two phases of the competition in a dominant performance in the first half.