Despite encouraging attacking play from the Foxes, who overcame Swansea City last week, Bassala Sambou's 48th minute strike condemned the visitors to their first league defeat of the campaign.
City’s starting line-up included seven changes from the Premier League International Cup loss to Reading on Friday, with Filip Benković, Callum Elder, Kiernan Dewsbury-Hall, Hamza Choudhury, Andy King, Fousseni Diabaté and Bartosz Kapustka all coming in.
Two of the new faces, Diabaté and Dewsbury-Hall, had attempts on goal early on, with the latter sending an audacious effort from distance just wide of João Virgínia’s left post.
Exhibiting a brand of football similar to the one associated with Claude Puel’s first team, the Foxes were expressing themselves in the final third in the drizzly Merseyside conditions.
Attacking trio Diabaté, Kapustka and Layton Ndukwu linked-up smartly on several occasions while Dewsbury-Hall seemed to benefit enormously from playing alongside Wales international King.
Choudhury, meanwhile, won a free-kick just outside the area in the 25th minute, but Ndukwu’s fearsome attempt whistled inches over the Toffees’ cross bar.
Another opportunity came Ndukwu’s way moments later when King floated a lovely ball into his path, teeing him up to volley it goalwards. However, his effort drifted just wide.
At the other end, the hosts’ only significant moment of the first half arrived with nine minutes to go as Nathan Broadhead located Sambou, but his shot flew over the bar.
Just after the break, it was Everton who took the lead, as Joe Williams found Sambou with an impressive through ball before the 20-year-old slotted it past the impressive Viktor Johansson.
Minutes later, Johansson, who played so well against Swansea a week previously, was called upon to keep an Anthony Evans free-kick out with an outstanding save.
As the clock ticked down, Senior Professional Development Phase Coach Steve Beaglehole looked to the bench with Louis Ramsay, Ryan Loft and Raúl Uche Rubio all coming on.
It could have been so different had Virgínia not been able to parry Loft's late attempt beyond the far post, but the hosts defended their lead stoically in the latter moments.
Major moment…
In what eventually turned out to be the only goal of the game, the Club's Under-23s would have been especially disappointed to concede so early into the second period.
It was a well-taken goal from Bassala Sambou, but it ultimately turned the tide in Everton's favour after a promising start from the visitors.
Who impressed?
Goalkeeper Viktor Johansson won deserved praise for his contribution to City’s clean sheet in the opening day 1-0 success over Swansea City last Monday.
Despite conceding in Merseyside, the 20-year-old Swedish shot-stopper was once again in fine form – making a sublime save to deny Anthony Evans from a 22-yard free-kick.
Coming up…
The live LCFC TV coverage of City’s Premier League 2 campaign continues on Monday as the Under-23s host Blackburn Rovers at Holmes Park for a 7pm BST kick-off.
The details...
City: Johansson, Knight, Benković, Elder, King, Choudhury (c) (Uche Rubio 72), Dewsbury-Hall, Johnson (Ramsay 59), Kapustka, Ndukwu (Loft 65), Diabaté
Subs not used: Stolarczyk, Kaba Sherif