City were without international quartet Alex Pascanu, George Thomas, Daniel Iversen and Darnell Johnson while the Sky Bet League 2 side made eight changes from their 1-0 win at Crawley.
Despite a gulf in experience between the two sides, it was the Foxes who dominated the early proceedings with a succession of industrious advances into the Cumbrians’ half.
Ndukwu, 19, in particular was a continued threat for the visitors, trying his luck on three occasions inside the opening 10 minutes, sending them wide of the near post from the right.
After 19 minutes, the young winger registered his first goal of the season, though, by latching onto Josh Eppiah’s smart ball across the box before sliding it into the bottom corner.
Steve Beaglehole’s young side were showing pace and urgency in their play, taking the match to Keith Curle’s men and keeping shot-stopper Shamal George on his toes.
While City were largely in control during the opening 45 minutes, they were reminded of Carlisle’s quality shortly before the interval when Tom Parkes guided his header onto the post.
Early in the second half, Leicester very nearly doubled their advantage when Eppiah twice dispossessed his man and forced Danny Grainger into a last-minute block.
At the other end, young Foxes goalkeeper Max Bramley, deputising for Iversen, had to make an outstanding stop from Sam Cosgrove’s thunderous half-volley to keep the hosts at bay.
Second half substitute Khanya Leshabela made his presence known with 20 minutes remaining, aiming a long-range drive narrowly wide of George’s bottom corner.
At the very end, Bramley made another brilliant stop to deny Reggie Lambe from point blank range, an intervention which ultimately secured all three points for the guests.
Major moment
It was a stroke of luck which, had it gone the other way, may have proven to be the spark for Carlisle to mount a comeback.
When Parkes hit the upright just before half-time, Kiernan Dewsbury-Hall was able to scramble it away. Fine margins indeed, but in City’s favour.
Who impressed?
Against more senior, Football League defenders, Ndukwu ran amok on the flanks for the Foxes, acting as Carlisle’s tormentor-in-chief for much of the match.
The former England Under-17s international was City’s main outlet and applied a neat finish to a devastating counter early in the first half to send Beaglehole’s men on their way.
Where does it leave us?
City sit in third place in Northern Group A, level on points with Carlisle and three behind leaders Fleetwood, ahead of next month's visit to Morecambe.
The top two sides from each pool qualify for the knockout phase.
Coming up…
City next contest a Premier League Cup group stage tie at Oakwell against Barnsley on Tuesday afternoon (2pm kick-off) before travelling to the capital on Friday.
Tottenham Hotspur will be their hosts in Premier League 2 at the north London club’s training ground (1pm kick-off).
The numbers...
Carlisle: George, Miller, Grainger (c), Liddle, Parkes, Jones (Adams 75’), Devitt, Nabi (Joyce 63’), Bennet, Cosgrove (Miller 63’), Lambe.
Subs not used: Bonham, Hope, Brown, Etuhu.
City: Bramley, Knight, Hughes, Wood, Kaba Sherif, Choudhury (c), Dewsbury-Hall, Ndukwu (Leshabela 67’), Gordon, Muskwe (Shade 89'), Eppiah (Ughelumba 71’).
Subs not used: Yates, Martis, Uche Rubio, Heaven.
Goal: Ndukwu 19’.
Referee: Ben Toner.
Attendance: 1,009.