Sammy Braybrooke's sensational free-kick edged the away side ahead at the AMEX Elite Football Performance Centre, before Julio Enciso levelled matters prior to the half-time interval. A second-half brace from Andrew Moran, though, secured success for the Seagulls.
Following a 2-2 draw with Celtic in the Premier League International Cup last Wednesday, coach Ben Petty made three changes from that XI, with experienced trio Lewis Brunt - who captained the side - Braybrooke and Kasey McAteer coming in for Bayli Spencer-Adams, Kian Pennant and Terell Pennant.
Brighton ran out comprehensive winners when the sides last met, earlier this term, and the hosts began on the front foot in this one, looking to impose their high-tempo passing game on the Foxes.
Enciso spurned a golden opportunity to break the deadlock eight minutes in. Collecting Imari Samuels' centre, the forward took a touch before attempting to find the bottom corner, but was unable to hit the target.
City worked their way into the game and good endeavour from Wanya Marcal-Madivadua down the right allowed McAteer time to pull the ball back for Tawanda Maswanhise, who sent his effort wide, before Brunt's strong run into the box set up McAteer, though he directed his effort straight at Tom McGill.
Attempts on goal continued to be created as Marcal-Madivadua won possession high up, intercepting the Brighton 'keeper's short pass, and was able to get a shot away, but one that the onrushing McGill palmed away to safety, making amends for his error.
A flurry of Brighton chances followed. Chituru Odunze beat Enciso's strike away, before Andrew Morgan volleyed the rebound over the top of the bar. Enciso then headed narrowly wide, while Jack Hinshelwood met Samuels' latest cross, also diverting his header off target, though Odunze looked to have it covered had the ball dropped the other side of the post.
However, it was Leicester who went in front, courtesy of a stunning set piece from Braybrooke, curling his free-kick into the top corner from 25 yards out.
Brandon Cover was kept out by McGill shortly after the goal, denying the away side a two-goal advantage, and they would soon rue that miss.
Enciso remained Brighton's biggest threat going forward and a left-footed strike, held by Odunze, was his latest tester. Odunze did brilliantly to keep Moran's header out, but could not prevent Enciso from turning Jack Spong's corner home at the front post just before half-time.
With all to play for in the second half, Cover's side-foot volley failed to trouble McGill once Brunt nodded Braybrooke's corner into his path.
The young Foxes stayed on the front foot and when Joe Wormleighton whipped in an inviting cross from the right, McAteer was able to meet it, heading wide via a deflection.
Not taking chances was to be Leicester's downfall once again, as the Seagulls completed their comeback via Moran's fifth goal of the season, turning Samuel's low cross home from close range.
He would soon add his second and Brighton's third, tapping in after Enciso's initial effort came back off the post.
Zach Booth came on for Khanya Leshabela, with Deniche Hill soon introduced in place of Cover, as the visitors chased an opening to get back into the game.
McAteer soon drove forward, collecting Braybrooke's through ball, but pulled his shot wide, while back at the other end, Moran, now on a hat-trick, scooped Samuels' lay-off over the top of the bar.
Enciso played Moran through minutes later and once the attacker took a good first touch, he looked odds on to score, but fired wide under pressure from Brunt as he searched for another.
With Leicester throwing more bodies forward, gaps opened up and, after Brighton captain Spong's free-kick hit the bar late on, substitute Jamie Mullins took aim, but Odunze saved.
There were half chances for City as the clock ticked towards 90 - Marcal-Madivadua striking straight at McGill, and Maswanhise also finding the shot-stopper in the way, but by then the points were all but secured by the home side.
Major moment – The turnaround
In a promising position having taken the lead, the Foxes' youngsters could not turn that advantage into a positive result, conceding twice in quick succession midway through the second half to ensure the points stayed in Brighton.
Where do we stand? – 14th in PL2
Leicester sit 14th in the PL2 standings following today's result, on 10 points from 15 games played, while Brighton are ninth on 19 points.
Coming up – Palace at home
City's next Premier League 2 encounter is back on home soil, against Crystal Palace Under-21s, as the Eagles travel to LCFC Training Ground on Monday 13 February (7pm GMT kick-off).
The details...
City: Odunze; Wormleighton, Appiah, Brunt (c), Flynn; Braybrooke (Godsmark-Ford 80'), Leshabela (Booth 65'), Cover (Hill 76'); Marcal-Madivadua, Maswanhise, McAteer.
Subs not used: Doherty, Spencer-Adams.
Goal: Braybrooke 38'.
Images: Brighton & Hove Albion FC.