Despite being second-best at times, Warren Joyce's side went ahead with a Tom Thorpe header and, after conceding an equaliser to Conor Newton, substitute Tom Lawrence grabbed a winner that sends the Reds above their opponents in the table.
A flat first half saw United fail to trouble Jak Alnwick in the home goal while the Magpies made a promising start. Xisco forced a diving stop out of Jonny Sutherland after only 32 seconds and there was a scare from a Marcus Maddison corner that drifted just past the far post.
Bebe got his shot all wrong after some tigerish work by Larnell Cole but the Reds struggled to get any sight of goal despite the game's outstanding player Thorpe leading by example as a powerhouse presence in midfield. Newcastle looked the likelier scorers but Brad Inman and Romain Amalfitano could only shoot at Sutherland following threatening breaks.
Xisco was guilty of a bad miss when scooping over the top after being teed up by Mehdi Abeid as Willie Donachie's side monopolised the chances in the opening half. Federico Macheda collected a pass from Adnan Januzaj but hammered a left-foot shot well off target and Bebe saw an effort loop over via a deflection but Alnwick headed into the interval totally untested.
Yet it took United less than two minutes to break the deadlock at the start of the second period. Januzaj flighted over a corner from the left that allowed skipper Thorpe to rise and despatch a top-class header past Alnwick and into the corner of the net.
The Tynesiders' immediate response was a Newton drive that fizzed well wide and Warren Joyce