The Blues are generally regarded as having one of the best youth set-ups in the country, with some justification, but a bizarre own goal by Nortei Nortey proved decisive in pleasant weather in the North West.
There was not a great deal between the two sides but Chelsea had the best attempt of the first half when captain Alex Davey fired a splendid shot just wide of Jonny Sutherland's goal.
Two substitutions and a tactical adjustment, that led to Jack Barmby playing in an unfamiliar wing-back position, helped United find some rhythm. Soon after the break, Byrne was presented with a one-on-one opportunity but Ben Killip pulled off a good stop.
Joe Rothwell was through in similar circumstances but was denied by a defensive block and the Reds were unlucky not to score when Byrne stretched to meet an Andreas Pereira cross but saw the ball hit a post and roll to safety.
The pressure eventually told as James Weir released Byrne again and Nortey rushed back but his backpass bobbled past Killip for a calamitous own goal.
After Byrne passed up an opportunity to wrap up the victory, Chelsea piled on the pressure towards the end and went closest to grabbing an equaliser with a George Cole drive that swerved off target.
United: Sutherland; Love, McNair, Grimshaw, Evans (Barmby 46); Weir, Pearson, Rothwell (A.Pereira 66), Rudge, Daehli, Wilson (Byrne 46). Subs not used: J.Pereira, Ioannou.