The Magpies had led the game 3-0, but it was Red Devils striker Will Keane who was the hero with four goals on the night to turn it around for the his side.
United went on to win the game and claim the title at Newcastle with a total of 14 wins from 18 games.
The side now have four games left to play in their domestic season, starting with the North-West derby against Liverpool on Thursday night.
The side will then line up in the national play-off final against Southern league winners Aston Villa.
Young Keane has contributed 17 goals and eight assists for the second string so far this season and made his first-team debut earlier this season against Blackburn Rovers.