United played well in what was a tight game against Boro, but three quickfire goals around the hour-mark put the hosts in the driving seat.
It had been goalless at half-time, but the scoring spree settled home nerves.
Ryan Carr bagged a great goal to register for the visitors, but Boro held on to claim their win.
"I'm really pleased with the way the lads worked hard and never gave up, even after Middlesbrough got their goals," youth boss Mark Birch said.
"It was very even, and we played some good football. Credit to them for the way they opened things up, but heads didn't drop and there's a lot we can take from it.
"Carrsy's goal was excellent, and we definitely have a lot we can work on, as well as areas we can look at to improve."