The early tempo of the game was upbeat, Boro going close through Alex Pattison who struck the side netting with a low drive from the edge of the box.
United settled and took the game back to Boro, but they couldn't find a way through and their attempts to test Zak Hemming, making his debut at this level in the Boro goal, were thwarted.
Boro almost took the lead with 20 minutes played as a well-worked free-kick set up Jo Wheatley to loft a ball into the box and Hayden Coulson hit the bar with a right-footed effort.
It was the visitors who struck first. With 29 minutes played Dan Barlaser, just up from the right-hand edge of the Boro penalty area, delivered a free-kick and Tom Heardman bundled home from close range at the second attempt.
Sticking to their task, Boro tried to work their way back into the game, but it was United who struck again.
With 39 minutes played Hemming made an excellent save to keep out a Heardman header, but Adam Wilson was on hand to tuck home from close range.
Only a very smart save from Nathan Harker in the Newcastle goal prevented Marcus Tavernier from reducing the arrears in the early exchanges of the second half, an acrobatic tip over coming from an edge of area shot.
Boro stuck at it, enjoying the majority of possession in a second half that brought a succession of corners.
Dan Ward went close for the Magpies, but that was a rare foray, breaking free from Boro pressure that brought a chance for Pattison who saw a low drive cleared off the lone by central defender Owen Bailey with Harker well beaten.
Bradley Fewster, a half-time change for Mikael Soisalo went close, while Marcus Tavernier looped a header just over, but the final game of the season for the U23s was to end in defeat and with Boro down to ten men after a red card was shown to Callum Johnson for a challenge in the second minute of added on time.
Boro Hemming; Johnson, Husband, McGhee (Capt.), Fry, Wheatley, Soisalo (Fewster 46), Tavernier, Mondal, Pattison, Coulson. Subs Bryn (gk); Elsdon, Silva Torrejon, McGoldrick.
United Harker; Williams, Gibson (Varney 69), Hunter (Capt.), Bailey, Findlay, Holmes (Newberry 90), Barlaser, Heardman, Ward (Sorensen 69), Wilson. Subs Huuhtanen, Broccoli
Scorers Heardman 29, Wilson 39
Referee Joseph Johnson
Red Card Johnson 90+2, straight red for a foul
Yellow Card Wheatley 28, foul, Varney, 90+2, retaliation