Lee Barnard's headed goal eight minutes into the second half was enough to settle a fiercely-contested encounter on a blustery day at the Foxes' Belvoir Drive training ground.
Along with Paulo Gazzaniga and Tadanari Lee, Barnard was one of three senior players drafted into the side after a difficult start to the new Barclays U21 Premier League campaign.
And the trio certainly seemed to bring an added level of experience as the Development Squad ground out their second victory of the season.
Much of the first half was far from memorable, with Omar Rowe having the only real half-chances of the opening quarter-hour but his first shot went wide of the Leicester goal while his second – from a free-kick – was easily held by Foxes goalkeeper Adam Smith.
At the other end, Leicester winger Brendan Daniels drew a couple of simple saves from Saints stopper Gazzaniga but the home side were generally second-best in the early exchanges.
U21 Coach Martin Hunter was forced into a change midway through the half, with Lloyd Isgrove withdrawn after feeling tightness in his hamstring to allow Jake Sinclair the chance to impress from the bench.
Chances remained few and far-between though, with striker Barnard – who is not part of the First Team squad this season – registering an attempt on target just before the break, but his header from Jason McCarthy's cross was easily held by 'keeper Smith.
HALF TIME: LEICESTER CITY U21S 0-0 SOUTHAMPTON U21S
Hunter was again made to reshuffle his pack at the interval, with Lee having picked up a knock during the first period. Corby Moore came on in the Japanese's place.
There was much more urgency about Saints in the second period, and their added impetus soon paid off.
Sinclair did excellently to surge down the right and deliver a whipped cross from the right that was at the perfect height for BARNARD to power in a header and give Saints a 53rd-minute lead.
The pair combined well again just after the hour mark, with Barnard this time turning provider for Sinclair to shoot just wide of the Leicester goal.
Joe Dodoo, on as a 59th-minute substitute for the hosts, gave Southampton a scare soon afterwards but his low ball across the face of goal could not find any of his teammates.
That seemed to spur the Foxes on, with their experienced frontman Paul Gallagher seeing a shot fumbled wide by Gazzaniga 20 minutes from time.
Harry Panyioutou then had a header easily held by Gazzaniga, before the Foxes frontman came dangerously close to getting in on goal only to be denied by an excellent tackle from Saints captain Jack Stephens.
Leicester continued to up the ante as full-time drew closer, but it was Saints who almost scored the game's second goal. First Rowe had a fierce shot saved by Smith then turned provider as his low cross was inches away from being turned in by the onrushing Barnard.
There was still a big opportunity for the Foxes to level in injury time, but Gazzaniga was at his best to tip Neil Danns' shot wide before the resultant corner was hurriedly cleared by a resolute Saints defence.
FULL TIME: LEICESTER CITY U21S 0-1 SOUTHAMPTON U21S
Leicester U21s: Adam Smith, Ryan Watson, Albert Sesay (c), Ben Frampah (Callum Elder 46), Zoumana Bakayogo, Jak McCourt, Michael Cain (Rob Paratore 78), Neil Danns, Paul Gallagher, Brendan Daniels (Joe Dodoo 59), Harry Panayioutou. Unused substitutes: Liam Sharpe (GK), Archange Nkumu.
Southampton U21s: Paulo Gazzaniga, Jason McCarthy, Jack Stephens (c), Jordan Turnbull, Matt Targett, Harrison Reed, Jake Flannigan, Lloyd Isgrove (Jake Sinclair 27), Tadanari Lee (Corby Moore 46), Omar Rowe, Lee Barnard. Unused substitutes: Cody Cropper (GK), Fraser Colmer, Bevis Mugabi.
Referee: Daniel Meeson