An early strike from Fraser Hornby, a star of the Toffees side who overcame Apollon Limassol in the UEFA Europa League, gave the visitors the lead, before a brilliant late double from Yohan Benalouane.
Under-23s boss Steve Beaglehole made six changes from the side who dispatched Scunthorpe United in the Checkatrade Trophy, calling upon first teamers Benalouane, Eldin Jakupović and Ahmed Musa.
Despite a decent opening from the hosts, a period which included Musa being denied by young goalkeeper Joe Hilton early on, it was the visitors who took the lead after 23 minutes.
Hornby fresh from making his senior debut, cut inside Sam Hughes and Benalouane to find himself in on goal, giving Jakupović little chance of keeping it out with a tidy finish into the bottom corner.
The Foxes continued to battle, however, and they showcased the same resilience which has seen them go unbeaten in all competitions since the middle of September.
With just 10 minutes of the first half remaining, their hunt for an equaliser continued when George Thomas guided a free-kick over Hilton’s crossbar from a distance of over 30 yards.
It was an ultimately frustrating first 45 minutes for the hosts, who had only conceded twice at all home season before kick-off, but they emerged from the changing room intent on improving matters.
On the hour-mark, Congo international Yannick Bolasie continued his return from injury for the Toffees, replacing Dennis Adeniran, to give the visitors some added attacking threat.
Managed by David Unsworth, the man who led them to the title last term, Everton looked composed for large periods despite having already suffered defeat by City on two occasions this season.
However, they couldn’t have accounted for their hosts’ late exploits, with Benalouane first blasting it beyond Hilton before lobbing it over the young Toffees’ stopper in the final 10 minutes.
Major moment
“City seemed more composed in possession in the second half, their play flowed better and they got their reward.” – Dean Hammond, LCFC TV summariser.
The interval served as a useful stoppage for the hosts to revaluate their tactical stratagem with Beaglehole changing their shape and pushing more of his players into attacking positions.
It took until the 83rd minute for his switch to pay dividends, but Benalouane’s fine double ensured the Under-23s continue their excellent form.
Who impressed?
Aside from Hornby's goal, it was another strong defensive outing from City’s backline, with Hughes in particular impressing once again for Beaglehole’s young side at the Club’s training ground.
After the introduction of Alex Pascanu at the break, Hughes was pushed into a more advanced role and he continued to impress, giving the hosts a strong spine to build attacks upon.
Where does it leave us?
The Foxes climb back to second in the PL2 standings with 24 points from 12 matches, six below runaway leaders Liverpool, who have won 10 of their fixtures this term.
Coming up…
City are next in action in the Premier League International Cup for the visit of Legia Warsaw to Holmes Park on Thursday 14 December (7pm kick-off).
Then it’s an away trip to Leigh Sports Village to face Manchester United in Premier League 2 for a 7pm fixture on Monday 18 December in Premier League 2.
The details…
City: Jakupović, Knight, Hughes, Benalouane, Wood, Choudhury, Dewsbury-Hall (Muskwe 65), Thomas, Gordon (Pascanu 45), Eppiah (Ndukwu 77), Musa.
Subs not used: Kaba Sherif, Bramley.
Goals: Benalouane 83, 88.
Everton: Hilton, Jones, Garbutt, Feeney (c), Foulds, Charsley, Baningme, Hornby (Sambou 70), Adeniran (Bolasie 61), Henen (Evans 75).
Subs not used: Renshaw, Broadhead.
Goal: Hornby 23.
Referee: Alan Young