The midfielder came off the bench for only his second competitive outing for the Under-21s following a year out with a broken leg and scored with his first touch, planting home a header from Andros Townsend's cross to make it 2-1 with 12 minutes remaining.
The team pushed forward in the closing stages in search of an equaliser but were caught on the break in the first minute of stoppage time as Andreas Pereira raced clear to secure the points for United.
As has been the case of late, Townsend was joined by Harry Winks, Shaq Coulthirst and Milos Veljkovic in our starting line-up while United fielded goalkeeper Joel Pereira, Ben Pearson and William Keane - all back from loans at Rochdale, Barnsley and Preston respectively.
We had the first effort of note in the seventh minute when Winks won the ball and Coulthirst fed in to Townsend who shifted right and struck low, but Joel Pereira got down well to turn wide.
United, pressing high, got on top for 10 minutes and made it count.
Matthew Willock forced a fine save from Tom Glover from the right angle in the 11th minute but a carbon copy chance led to the opener just two minutes later. This time James Weir was played in down the right and Glover did well to get down to his shot but Keane was there to make sure on the line. Weir was later credited with the goal.
Keane dragged wide from 20 yards and Glover did well to touch the ball away from the United front man after a scramble from Willock's cross. Andreas Pereira also missed the target from the edge of the box.
We gradually got a foothold in the game but Coulthirst was often isolated and both Townsend and Anthony Georgiou well shackled down the flanks.
Townsend started to find space towards the end of the first half and provided the ammunition for Coulthirst to send an overhead kick just wide before hitting the woodwork himself just before the break. He left Joshua Harrop in his wake to burst into the box on the right side and then twisted left, right and left again before curling onto the crossbar.
We pushed further up the pitch as we tried to get back into the game in the second half but, as was the case for much of the first period, play stayed in the midfield areas as the teams cancelled each other out.
It wasn't until the hour mark that the next chance arrived when Timothy Fosu-Mensah headed wide from Andreas Pereira's deep corner but then disaster struck five minutes later as the same player curled another corner into the same area and this time the ball sailed over Glover's outstretched arm and nestled in the far corner of the net.
Will Miller replaced Winks on 71 minutes but United were now in the ascendancy and Keane fired narrowly wide from Andreas Pereira's pass.
Pritchard entered the action for Luke Amos on 75 minutes and made an immediate impact, darting between defenders to connect sweetly with a header from Townsend's cross and reduce the arrears.
The team found energy from the goal and pushed for an equaliser but again, chances were at a premium. Coulthirst came closest when his shot from 12 yards was blocked by Fosu-Mensah.
Everyone piled forward for a corner as the clock ticked into injury time but we were caught on the break as a clearance found Andreas Pereira breaking into open space from halfway and he made no mistake, skipping past Glover and slotting home.
Manchester United U21s: J Pereira, Varela, Williams, Fosu-Mensah, Weir (c), Pearson, Willock (Riley 58), Redmond, Keane (Fletcher 85), A Pereira, Harrop (Rashford 75). Substitutes (not used): Rothwell, O'Hara (GK).
Spurs U21s: Glover, Walker-Peters, Amos (J Pritchard 75), Lesniak, Carter-Vickers, Veljkovic (c), Townsend, Winks (Miller 71), Coulthirst, Walkes (Goddard 79), Georgiou. Substitute (not used): Voss (GK).