Wind caused havoc for both sides but it was the visitors who coped best and the Reds' defence will be disappointed that three crosses proved their undoing.
The defeat leaves United third in the Elite Group table, behind Southampton on goal difference and four points off Fulham, who also enjoy a game in hand.
The young Reds started well but lacked incisive passing in the final third. Jack Rudge hit the bar after neat work by Andreas Pereira but the Toffees took the lead on 24 minutes when a free-kick near the corner flag was headed towards goal by George Waring. Ben Pearson cleared from underneath the crossbar but the referee ruled the ball had crossed the line.
Everton doubled their advantage just five minutes after the restart when Ryan Ledson stole in at the back post to head home a wind-assisted cross.
The introduction of James Wilson for Jack Barmby on the hour mark provided United with extra spark but despite dominating possession the Reds couldn't breach the visitors' defence.
Instead, Everton added a third in injury time when Callum Dyson, unmarked at the far post, volleyed in another cross.
United: J.Pereira; Love, Grimshaw, McNair, Evans (Goss 82); Pearson, Barmby (Wilson 60), Rudge, Byrne; A.Pereira, Daehli.