Admiral Muskwe struck his sixth goal of the season on the stroke of half-time to cancel out Harry Wilson's opener before Hughes sealed all three points in added time at Prenton Park.
This latest success propels the Foxes up to third and extends their unbeaten run to seven matches in all competitions - six of which have been victories.
Under-23s manager Steve Beaglehole was ecstatic at full-time, heralding the work-rate and application of his talented squad, following yet another rewarding outing on Merseyside.
Leicester have so far defeated Everton, West Ham United, Chelsea, Hertha Berlin, Carlisle United, Barnsley, Swansea City and now Liverpool this term.
Beaglehole made just one change to the starting XI who dispatched Swansea on Monday with stopper Max Bramley making way for Eldin Jakupović in goal.
Within nine minutes of the referee’s whistle, the Foxes were handed a guilt-edged opportunity to take the lead when Kiernan Dewsbury-Hall’s low drive, from 18 yards out, was deflected just wide.
Despite the Reds boasting Danny Ings and Dominic Solanke among their ranks, Leicester went close again when Josh Gordon arrowed it narrowly over from just inside the area.
City’s pressure resumed with 23 minutes on the clock as George Thomas whipped a corner onto the head of Hughes, but the ex-Chester man nodded it wide of the near post.
It was Liverpool who went ahead after 28 minutes. Ings, continuing his return from injury, played in Wilson to tuck it into Jakupović’s bottom corner.
Things nearly got even better for the hosts shortly after when a fortuitous ricochet landed to Ings. The former Burnley striker, however, sent his half-volley over the bar.
With two minutes to go until the interval, the Foxes drew level when a headed flick from Hughes fell kindly to Muskwe to score his third goal in a week from close range.
City pressed for a winner during the second period and their efforts almost went rewarded on 52 minutes, although Gordon’s curler from 15 yards whistled beyond the upright.
It quickly opened up for Ings at the other end, following industrious wing-play from Matty Virtue, but Jakupović saved well at his feet to keep it 1-1.
While chances become less frequent in the latter stages, it only took one to hand City a huge victory on Merseyside.
When the ball fell to Hughes in the six-yard box, the 20-year-old's header was spilled by Kamil Grabara and trickled over the line, sparking joyous celebrations in the away dug out.
Admiral Muskwe wheels away after scoring City's first goal.
Muskwe’s form in front of goal has been vital for the Club’s Under-23s for almost two seasons and the 19-year-old continues to live up to his billing as City’s most potent attacking force.
His deft equaliser just before the break was a deserved return for another combative display and acted as a springboard for the Foxes to return to the East Midlands with three hard-earned points.
Leicester City Under-23s
Hamza Choudhury and Josh Knight congratulate Sam Hughes.
In a match which pitted City’s back four against a Liverpool forward three of Ings, Wilson and Solanke, the defensive quartet deserve praise for another steadfast display.
Ings, in particular, prowled the final third, but Hughes, Darnell Johnson, Josh Knight, and Connor Wood were at their best to keep him at bay.
Where does it leave us?
Sam Hughes is mobbed by his Foxes team-mates on Merseyside.
This result sees Beaglehole's men surge beyond West Ham into third place with a healthy tally of 17 points from nine matches.
Despite Liverpool winning seven of their nine league outings so far, City are now just four points adrift of the PL2 summit.
Hamza Choudhury competes with Danny Ings for possession.
City have over a week to prepare for their next competitive outing, a Checkatrade Trophy group stage clash at Sky Bet League 2 side Morecambe next Tuesday (7:45pm kick-off).
Beaglehole’s side need to emerge from with a positive result to give themselves a chance of reaching the knockout stages of the competition.
Liverpool: Grabara, Whelan (c), Juanma, Jones, Masterson, Brannagan, Ejaria (Dhanda 82'), Virtue, Ings, Wilson, Solanke (Kane 63’).
Subs not used: Johnstone, Firth, Adekanya.
Goal: Wilson 27’.
City: Jakupović, Wood, Knight, Hughes, Johnson, Choudhury (c), Dewsbury-Hall, Thomas, Muskwe, Gordon (Kaba Sherif 81'), Eppiah (Martis 88').
Subs not used: Bramley, Pascanu, Ndukwu.
Goals: Muskwe 43’, Hughes 90+2.
Referee: Andrew Miller
Images: Nick Taylor/Liverpool FC
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