A 3-1 reverse to Burton Albion on matchday one left Leicester with plenty to do in order to qualify for the knockout stages of the competition and it was another tough night against Sky Bet League 1 opposition at Sixfields Stadium.
Four changes from Friday's Premier League 2 victory over Aston Villa saw the young Foxes bring in Olabade Aluko, Joe Wormleighton, Oli Ewing and Michael Golding for Jahmari Lindsay, Jake Evans, Louis Page and Jeremy Monga.
But after a goalless opening half an hour, the hosts found a way through when on loan Brighton & Hove Albion midfielder Samy Chouchane set up Timothy Eyoma to score.
In the second half, a Neo Dobson double ensured it was the Cobblers who took all three points, moving to the top of Southern Group F as a result.
As for City, they require a win over Notts County in their final group stage fixture, and a goal difference swing, to progress in second place, with the match-up against the Magpies to take place next Tuesday, a 7pm kick-off at Meadow Lane.
They are next in action this Friday, meanwhile, travelling to take on Coventry City at Your Co-op Community Stadium in the Premier League Cup (7pm kick-off).
The details...
City: Bausor, Wormleighton (Evans 61'), Godsmark-Ford, Wilson-Brown, Aluko; Joseph, Cartwright, Ewing (Page 76'), Golding (Monga 60'); Alves, Pennant (King 71').
Unused subs: French, Hill, Amartey.