The young Foxes, returning to action following the international break, led 3-0 in Seagrave before the Addicks produced an extraordinary comeback during the final 20 minutes to claim all three group-stage points, just weeks after we had ourselves come from three goals down to draw with Blackburn Rovers.
Bobby Amartey got the scoring started for City 10 minutes before half-time and it only took Jake Evans 11 second-half minutes to double our advantage.
The 17-year-old then fired in another to complete his brace and looked to have put Leicester out of sight, but the visitors had other ideas.
Ethan Brown pulled one back almost immediately and Patrick Casey soon added a second to give the south Londoners hope of getting something out of the game.
Emmanuel Sol-Loza then equalised, but it would get even better for the away side, who won a late penalty, converted by Henry Rylah in the 87th-minute.
Brown started the Charlton comeback.
We remain fourth in PL Cup Group C, yet to get off the mark, and it's Ipswich Town heading to Seagrave on matchday three in the competition, on Friday 21 November. Up next in Premier League 2, meanwhile, it's Southampton at home on Saturday 25 October (1pm BST kick-off).
The details...
City: Donohue, Aluko (R. Donnelly 62'), Amartey, Gray, Ali; Motsi, Page (Akolbire 62'); Richards (Otchere 74'), Golding (Omobolaji 75'), Briggs; Evans.
Unused sub: Marson.
Goals: Amartey 36', Evans 56', 66'.