Carlos de Pena was on target twice in this Premier League International Cup tie. The result means Manchester United win the group by one goal and Boro must hope they qualify as one of the best runners-up to join their hosts and play in the knockout stages.
Early pressure from United, managed by Nicky Butt, had Boro pushed back but it wasn't until the 13th minute that Aynsley Pears was called into action when Joshua Harrop crossed from the right and Devonte Redmond headed for goal.
The effort had direction, but little power, pretty much like a penalty awarded to United with 15 minutes played following a foul from Julien de Sart.
Joshua Harrop took the spot-kick and Pears fell to his left to smother.
Undeterred, United kept up the pressure and a good run from right-back Matthew Olosunde ended with a low shot deflected just wide for a corner.
For all United saw more of the ball, Boro coped well with what was thrown at a them and were not shy of getting forward when they could. The problem was, that wasn't as often as they would like.
When Jordan McGhee was felled by Demetri Mitchell in the closing minutes of the first half, Boro were awarded a free-kick just up from the left-hand edge of the United penalty area.
The well-worked set-piece saw Carlos de Pena shape to shoot, but square to Bryn Morris who brought a full-length save from Sam Johnstone with a low shot from the edge of the box. From the resulting corner, Morris headed a half-decent chance off target.
Half-time United U23s 0 Boro U23s 0
There was a chance for Boro at the start of the second half when De Pena rose to meet a right-wing cross, but his header was comfortable enough for Sam Johnstone.
A minute later Boro were on the attack again, breaking down a United move to create a chance for Callum Cooke whose goalbound shot was deflected for a corner.
When de Pena intercepted a crossfield ball of the edge of the centre circle he attempted an audacious shot with Johnstone off his line. The effort was on target, but didn't carry enough height to clear the goalkeeper.
The opening goal came against the run of play, though in part Boro caused their own downfall by backing off an allowing Demetri Mitchell time to crack home into the roof of the net from 20 yards with 58 minutes played.
It didn't take Boro long to draw level as Jordan McGhee ended a strong run down the right with a low cross that picked out Carlos de Pena in front on an open goal with 62 minutes played.
There was more than an element of doubt about a second penalty awarded to United with 71 minutes played when Matthew Elsdon was adjudged to have fouled Tosin Kehinde. Harrop wanted to take the spot-kick, so too did Sean Goss and it took captain Axel Tuanzebe and Butt to make sure Goss took it. He did and beat Aynsley Pears with a powerful shot.
Harrop was substituted soon after, the cause of a fracas following a foul born out of frustration.
A second equaliser ensured a lively finish as, with 83 minutes played, Carlos de Pena, from out wide on the right, curled in a direct free-kick.
Manchester United: Johnstone; Olosunde, Mitchell, Tuanzebe (Capt.), Poole, Goss, Harrop (McIntosh-Buffonge 74), Willock, Redmond (Scott 81), McTominay, Gribbin (Kehinde 67). Subs: O'Hara (gk); Doughty, Warren.
Middlesbrough: Pears; McGhee, Elsdon, Morris, Kitching, De Sart (Jakupovic 72), Pattison (Maloney 80), Tinkler, Mondal, Cooke (Capt.), De Pena. Subs: Fryer (gk); Coulson, McAloon, Wheatley, Johnson.
Referee: Peter Wright
Yellow cards: De Sart 15, foul; Harrop 73, foul; De Pena 73, pushing; Tuanzebe 81, foul.