Looking to bounce back from a 3-2 league reverse at Blackburn Rovers ahead of the international break, the young Foxes turned their attention to the PL Cup but fell behind to a Jahmari Lindsay own goal on the half-hour mark in Seagrave.
Responding in the second half, Jayden Joseph's 58th-minute strike restored parity, but it wasn't to be enough to claim a share of the spoils, with Jack Thompson finding a winner for the visitors with 12 minutes to play.
The result leaves City third in Group B, remaining on three points after suffering their first defeat, with Coventry City still to play in the competition next month as the Foxes aim to progress into the knockout stages.
It's a quick turnaround for Leicester this week, meanwhile, with a trip to Chelsea coming up on Friday evening - a 7pm kick-off at Kingsmeadow back in Premier League 2.
The details...
City: French, Joseph, Godsmark-Ford (c), McAlinney, Lindsay; Onanaye (Hill 63'), Briggs, Alves (King 70'); Monga, Evans, Pennant (Amartey 82').
Unused subs: Bausor, Page.
Goal: Joseph 58'.