Visitors Everton had led after just 37 seconds through Martin Sherif, who netted another after Ethan Wheatley’s well-taken 10th-minute leveller.
The United striker, who became the club’s 250th Academy graduate last April, netted a second equaliser of the night shortly after half-time as the young Reds pressed high up the pitch.
Tyler Fletcher’s edge-of-the-box shot from a Sekou Kone pass put Travis Binnion’s side ahead and the latter midfielder then benefitted from a significant deflection to further extend the advantage.
United finished fifth in Premier League 2’s regular season, and will now look forward to another exciting knockout fixture.