It was a poor game until Ryan Ledson broke the deadlock with a fantastic goal of his own. But Everton were unable to hold on against their local rivals, and were soon back on level terms courtesy of a Dan Cleary header.
Wilson then rounded off the game three minutes into the allotted four minutes of injury time to send the Toffees home empty-handed.
The opening 45 minutes was one that lacked any sort of invention, and was a scrappy battle mainly fought in midfield.
But, really, the hosts should have taken a narrow lead into the second half thanks to Tyias Browning’s scuffed clearance in his own area.
It fell to Liverpool captain Cameron Brannagan in the box, but the midfielder blasted his shot against the crossbar, and Jerome Sinclair was unable to follow it up with a shot on target.
They also had a decent penalty shout when Jack Dunn went down in the box under pressure from Brendan Galloway, but referee Joseph Johnson was quick to dismiss Liverpool appeals.
And things didn’t get much better at the beginning of the second period, as neither side troubled going forward.
In fact it took almost 70 minutes for the game to come to life, as midfielder Ledson opened up the scoring with a sweet strike.
It was created from relatively little, as Gethin Jones won the ball off Joe Maguire. He then found Ledson as Everton broke forward, and the Liverpool-born player looped the ball over a helpless Vigouroux from all of 20 yards.
And like the old London bus analogy goes, you wait a long time for one, and then two come at once, and that’s how this game played out.
It took just four minutes for Liverpool to level things up, as substitute Wilson’s free kick was headed back across goal before being turned in by Cleary from point-blank range.
Everton’s goal opened up the game, and the Reds came close five minutes from time, but no-one could get on the end of Wilson’s cross as it flashed across the face of goal.
But Liverpool had the last laugh, as Wilson’s sublime strike left Russell Griffiths gazumped in the Everton goal, dealing the young Blues a cruel blow.
The win propels Liverpool into second place in the standings, whilst Everton remain seventh for the time being.
Liverpool U21: Vigouroux (GK), Williams, Maguire, Jones, Sakho (Smith, 46’), Stewart, Canos, O’Hanlon (Cleary, 32’), Sinclair, Brannagan, Dunn (Wilson, 64’) Subs: Fulton (GK), Trickett-Smith, Wilson, Cleary, Smith
Scorers: Cleary (73’), Wilson (90 +3')
Bookings: Williams (59’)
Everton U21: Griffiths (GK), Kenny, Connolly, Junior, Browning, Galloway, Jones, Walsh, Henen, Ledson, Green (Dowell, 66’) Subs: Hunt (GK), Dowell, Langton, Donohue, Bainbridge
Scorers: Ledson (69’)
Referee: Joseph Johnson