After Alex Denny had handed the Toffees a 70th minute advantage at Holmes Park, Academy products Kairo Edwards-John and Hamza Choudhury, from the penalty spot, struck late for City.
As a result, the Foxes end their Group F campaign as pool winners while also maintaining their season-long unbeaten record in Whetstone ahead of this week's last-16 draw.
Under-23s manager Steve Beaglehole made five changes from the 3-1 Premier League 2 win over Arsenal with Max Bramley, Simran Thandi, Alex Pascanu, Layton Ndukwu and Liandro Martis all in.
After impressing for the Club’s Under-18s this season, Thandi’s appearance in the starting line-up was a notable one; his first start for City’s Development Squad.
It took until the 24th minute for either side to challenge the opposition goalkeeper as Everton’s Conor Grant forced Bramley into a smart low save from outside the area.
City eventually started to pose more of a threat. First Ndukwu’s shot was blocked by Luke Garbutt before Josh Eppiah’s low drive, from 18 yards, led to a last-ditch Beni Beningime intervention.
Against the reigning Premier League 2 champions, a throne Leicester are in contention to claim for themselves this term, the hosts were finding it difficult to carve out clear-cut opportunities.
Harvey Barnes was lively on the left flank and, shortly after the restart, the Countesthorpe-based youngster galloped down the channel and almost forced an own goal from Garbutt.
With 20 minutes remaining, the Toffees took the lead. Substitute Anthony Gordon charged down the left before finding Jose Baxter who, in turn, laid it on for Denny to rifle it into the bottom corner.
The match presented an opportunity for Beaglehole to hand Tyrese Shade, Khanya Leshabela and Edwards-John rare action for the Under-23s with all impressing in chilly conditions.
On 85 minutes, Sam Hughes nodded it down for Edwards-John to start the comeback with the Foxes youngster able to bundle it past visiting goalkeeper Mateusz Hewelt at the far post.
When Everton captain Antony Evans was adjudged to have handled in the area, meanwhile, Choudhury stepped up to send Hewelt the wrong way from the spot with just two minutes remaining.
Who impressed?
Making his bow at Development Squad level, right back Simran Thandi delivered an assured and comfortable display on a big night for the 18-year-old.
An impressive figure for the Academy side, who sit sixth in the Premier League U18 South standings, Thandi did his chances of further Under-23s action no harm at all with an enterprising display.
Where does it leave us?
City finish the campaign top in Group F with 14 points, four above Everton, and they will discover their last-16 opponents when the Premier League Cup last-16 draw is made later this week.
Coming up…
A top-of-the-table PL2 clash with Liverpool awaits on Monday at King Power Stadium (7pm kick-off) - which you can watch live on LCFC TV and in-person with tickets on sale online now.
The details…
City: Bramley, Thandi, Pascanu, Hughes, Wood, Choudhury (c), Dewsbury-Hall, Ndukwu (Edwards-John 81), Barnes, Martis (Leshabela 66), Eppiah (Shade 66)
Subs not used: Yates, Husek,
Goals: Edwards-John 85, Choudhury (pen) 88
Everton: Hewelt, Markelo, Garbutt (Sambou 59), Baningime (Gordon 59), Ouzounidis, Gibson, Evans (c), Denny, Lavery (Bramall 59), Baxter, Grant
Subs not used: Hilton, Astley
Goal: Denny 70
Referee: Daniel Maddleton
Attendance: 286