Admiral Muskwe opened the scoring for the Foxes in the ninth-minute, but Brennan Johnson's brace, either side of a Jamie Ward strike, sealed three points for the home side.
City’s line-up included three changes from last week’s 1-1 draw at Exeter City with goalkeeper Max Bramley, midfielder Kiernan Dewsbury-Hall and forward Khanya Leshabela coming in.
As a result, shot-stopper Viktor Johansson and striker Ryan Loft dropped to the bench, while midfielder Callum Wright was not named in the matchday squad.
Meanwhile, Forest’s side was an experienced one with Liam Bridcutt, 29, and Ward, 32, among their ranks for the clash in Alfreton.
Within the first 60 seconds, the home side nearly took an early lead as Jake Taylor powered a half-volley towards Bramley’s goal, but it cannoned back off the base of the post.
Despite a commanding opening spell from Forest, it was City who went ahead in the ninth minute as Dewsbury-Hall found Tyrese Shade on the right flank, who played it in for Muskwe.
The Zimbabwe senior international made no mistake inside the 18-yard box with a first-time finish to score his fifth goal of the 2018/19 campaign in all competitions.
Leicester’s strategy was disrupted in the 18th minute, though, when right-back Louis Ramsay picked up a knock which necessitated a change, as Under-18s defender George Heaven came off the bench.
While there were few major opportunities to comment on in the opening 45 minutes, Forest did deservedly level the scores before the interval.
When Muskwe was adjudged to have bundled Johnson in the penalty area, the home side’s young forward stepped up and sent it into the bottom left corner.
It was 2-1 to Forest five minutes into the second half as Arvin Appiah spotted the run of Ward, who collected the ball calmly and slotted it in to turn the match on its head.
City's response to that disappointment, though, was impressive and they chased loose balls, harried their opponents in the midfield and created several scoring chances.
Layton Ndukwu looked brighter as the match progressed and his silky runs into the final third kept Forest's defence on their toes into the latter moments.
However, it was Forest who found the net again with three minutes to play as Johnson was played into space behind the backline and finished well past Bramley to seal the points.
Having not featured for the Club's Development Squad since a 2-0 win at Derby County in September, Layton Ndukwu's recovery from a back complaint continued on Thursday.
The 20-year-old, who can operate on the wing or through the middle, marked his second start of 2019 with a performance defined by attacking endeavour and skilful industry at Impact Arena.
Where does it leave us?
City finish second in Group D of the Premier League Cup, on six points, and owing to their stronger goal difference over Exeter City, will progress to the competition’s Last-16 stage.
The Foxes head to the Academy Stadium on Sunday afternoon to face Manchester City in Premier League 2 Division 1 (1pm GMT kick-off).
City: Bramley, Ramsay (Heaven 18’), Ughelumba, Kaba Sherif, Hughes (c) (Loft 45’), Pascanu, Leshabela, Dewsbury-Hall, Muskwe, Ndukwu, Shade
Subs not used: Johansson, Meite, J. Gyamfi
Goal: Muskwe: 9'
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