The Reds were behind in the 13th minute and then slipped to a 2-0 deficit just after the break. But a superb turnaround in the quality of performance led to Nicky Ajose, John Cofie and Etzaz Hussain providing the goals for a spirited fightback.
Paul McGuinness was able to select Reece Brown, Zeki Fryers and Etzaz Hussain after lengthy spells on the sidelines. But the U18s coach clearly had one eye on Thursday's FA Youth Cup fifth round tie with Blackburn Rovers as he named key men Will Keane and Paul Pogba on the bench.
United started well but a collison between goalkeeper Sam Johnstone and defender Scott Wootton, which left the Reds stopper understandably shaken, seemed to knock the home side out of their stride. While there were no visible side effects to Johnstone's performance after a nasty fall, he was unable to keep out Andy Nichols' looping header on 13 minutes.
It was a scrappy half with the rhythm and attacking potency of United's recent display in the 5-1 FA Youth Cup win over Burnley sadly lacking. But the introduction of influential midfielder Pogba at half-time made a huge difference.
However, again despite a promising start, Stoke struck once more to dampen United spirits. A dangerous cross came in from the right and Brown headed into his own net.
It wasn't until after the hour mark that United's courageous comeback began. The breakthrough arrived when Ajose was fouled in the box, dusting himself down before coolly converting the kick.