Forward Amani Richards scored both Leicester goals to lift the side up into sixth position in the table and onto 22 points from 17 matches played.
Following a heavy defeat to Crystal Palace 10 days prior, the young Foxes returned to the capital for their latest league outing at Arsenal Training Centre, with coach Adam Barradell making one change to that XI.
After a goalless first half in Shenley, the visitors seized the initiative shortly before the hour-mark when Bradley Ibrahim converted a 57th-minute penalty for the Gunners.
Set up by Freddie Cook, Richards levelled the scores with just over a quarter of an hour to play, before both sides were reduced to 10 men in the closing stages.
First Arsenal's Coby Small received his marching orders from referee Teddy Osborn and a minute later Kevon Gray was shown a second yellow card for the visiting Foxes.
Leicester were not to be denied though and once Richards, assisted by substitute Joshua King, netted his second of the game to complete the second-half turnaround in the final minute of normal time, the away side held on to claim a dramatic three points.
Next up in the league for City's youngsters is a home fixture against fifth-place Chelsea on Saturday 15 April, an 11am BST kick-off at LCFC Training Ground.
The details...
City: Addai; Cook, Grist (C), Gray, Ali (McAlinney 68'); Joseph, Lewis, Nyoni, Fisken (King 60'), Briggs; Richards (Ononaye 90+2').
Subs not used: French, Thomas.
Goals: Richards 73', 88'.