Anfernee Dijksteel made his return from injury, but Boro's Under-23s' five-game unbeaten run came to a halt with a defeat to Newcastle United.
Dijksteel got an hour under his belt in his first competitive minutes since the win at home to Barnsley back in November,
Elliot Anderson bagged the first for the visitors, before Thomas Allan notched the second.
Newcastle had a gilt edge chance to take the lead with less than 10 minutes gone as Anderson came onto a cut back on the edge of the box, but there wasn't enough conviction behind his strike to trouble Dejan Stojanovic.
Captain Tyrone O'Neill took aim from outside the box but his attempt looped over the bar, and he played his part in teeing up Mitchell Curry for a big chance as he nodded it into his path, but his strike was excellently tipped around the post by Jake Turner in the visitors' goal.
The away side applied most of the pressure in the first period and Oisin McEntee rose highest from a corner with over half an hour gone, but it was high over the crossbar.
Anderson and Liam Gibson went close to breaking the deadlock for Newcastle inside the final few minutes of the first period, as the former curled an effort wide from outside the box before the latter was wide from an acute angle.
O'Neill sent Daniel Dodds clear down the right in the opening minutes of the second half, the winger cut it back for Curry who teed up O'Neill to strike from the edge of the box, but Turner had it covered.
The breakthrough came with a little over ten minutes gone of second 45 action, as Anderson twisted and turned inside the box before driving low into the bottom left corner.
And Newcastle doubled their advantage after the hour with a slick move as Jack Young slid a well-weighted pass through for Allan to score from a narrow angle.
Chances for Boro were limited, and a Harry Green effort from the edge of the area kept out by Turner as he punched it clear.
Nathan Wood was dismissed deep into second half stoppage time as he brought down a Newcastle man and was deemed to be the last man.
Graeme Lee's side head to the Leigh Sports Village next in the league on Monday March 16 to face Manchester United.
Boro: Stojanovic, Dijksteel (Balde), Wood, Hood, Robinson, Dodds, Sykes, Wearne, Curry (Green), Burrell, O'Neill. Unused subs: Cornet, Metcalfe