However despite the defeat, latics remain four points clear of struggling Bolton at the bottom of the table.
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Liverpool started the match with Jack Hobbs, Godwin Antwi, Paul Anderson and Miki Roque who all recently helped the club gain FA Youth Cup semi-final success. But the most high profile inclusion was that of Kop hero Robbie Fowler who played a key role in the opening half.
Latics started the game well and should have taken the lead after 23 minutes when Connolly dashed down the left wing to put through Andreas Johansson who blazed the ball over the bar from close range.
Johansson's night got worse after 37 minutes, heading wide from eight yards out after an excellent cross from winger David Owens.
However on the stroke of half-time Liverpool took the lead with a Robbie Fowler tap in. The striker reacting swiftly to score from two yards out after veteran keeper Gary Walsh struggled to keep hold of a Jack Hobbs header.
Fowler was replaced at half-time by Welsh under-21 international Ramon Calliste who came close to extending the lead after 50 minutes when his headed effort was well dealt with by latics full back James Heywood.
Liverpool eventually doubled their advantage in the 65th minute when Scotland Under-21 international Robbie Foy drilled home from the edge of the 18 yard box.
Latics tried hard to fight their way back into the game and their best chance came to Republic of Ireland International David Connolly who forced Liverpool keeper David Martin into a brilliant save in the 77th minute, which guaranteed his side the points.
The reserves' next game is on the 29th March at home to Wolves, kick off is 7:45pm
Teams:
Liverpool:
Martin, Barragan, Smith, Antwi, O'Donnell, Roque (Flynn 80), Anderson, Hobbs, Fowler (Calliste 45), Guthrie (Lindfield 84), Foy
Unused Subs: Woods, Lancaster (GK)
Wigan:
Walsh, Heywood, Waterhouse, Lee, Jakcson (Roberts 76), Francis, Owens (Stephan 73), Mahon, Johansson, Connolly, Ziegler
Unused Subs: Croll, Smith, Montrose
Goals:
City: Fowler 45, Foy 65