Gyliano van Velzen created both goals in the first half as the Tynesiders, who are well clear in Group D of the Academy League, suffered a rare defeat.
Dan Taylor had already flicked against the bar for the visitors from a corner when the Reds took an early lead. Seconds after the scare, Jack Barmby fed van Velzen and the Dutchman tricked his way into a position to cross for Ben Pearson to slide in for a finish extremely similar to the one James Wilson scored late on to beat Charlton in the FA Youth Cup at Old Trafford.
The Magpies worked hard to get back on level terms and probably deserved their equaliser on 34 minutes when Ben Sayer's dangerous free-kick was nodded past debutant keeper Kieran O'Hara by Taylor. However, United restored the lead before the break following another fine run by van Velzen. The wide man left three defenders in his wake to centre for Jack Rudge to bullet past Jonathan Mitchell in the visiting goal.
The second half was a tight affair with Rothwell, who produced a polished performance on his return from injury, curling wide and Liam Grimshaw and Barmby also off target from half-chances. At the other end, O'Hara was equal to everything thrown at him and denied Taylor following one smart move. Substitute Brandon Miele also forced a decent stop out of the Reds keeper as Paul McGuinness' side held out.
In stoppage time, Pearson released substitute Sam Byrne, who was felled by Mitchell after rounding the keeper, but the Magpies' No1 was able to atone by pushing away Rothwell's spot-kick.