The Seagulls were back to their exciting best following a difficult night in the North East against top-four hopefuls Newcastle United on Thursday, with a glut of the hosts' star players returning to the starting lineup.
Evan Ferguson was one of the incomings into the Brighton side, and the 18-year-old bagged a first-half brace to put Roberto De Zerbi's men into a deserved two-goal lead at the interval.
A largely lacklasture Saints side rallied slightly at the start of the second period and managed to score via Mohamed Elyounoussi's header, however Brighton quickly squashed any fears of a collapse with Pascal Gross scoring the hosts' third of the afternoon.
Today's loss for Southampton confirms they will finish bottom of the Premier League standings in a season in which a high managerial turnover and departure from their identity has cost them so dearly.
Brighton were good value for their commanding lead after the first half but had plenty of opportunities to be even further ahead of their South Coast counterparts, with Kaoru Mitoma firing narrowly wide of the Saints' net after driving into the box.
The Japanese winger has impressed during his maiden term for the Seagulls and had another glorious chance to break 10-game drought in front of goal when he latched onto a poor Alex McCarthy pass and raced into the area, however the 26-year-old's chipped his effort onto the post.
The hosts' dominance of possession and chances would soon be rewarded when Alexis Mac Allister found youngster Ferguson in space, with the Irishman's low-drilled shot going through the legs of Lyanco and squirming under the body of McCarthy - the 33-year-old stopper should have done better.
Just over 10 minutes later De Zerbi's charges had their second of the afternoon - Mitoma showed speed and strength on the left flank as he carried the ball from inside his own half before playing a perfectly-weighted pass into the path of Ferguson, with the striker making no mistake with his first-time finish.
Southampton improved significantly in the early stages of the second half and netted their 32nd goal of the Premier League season through Elyounoussi's glancing header.
James Ward-Prowse - one player in the Saints squad that is undeniably top-flight quality - delivered a wicked corner into the Brighton box which the Norwegian winger flicked over Jason Steele to give the visitors a glimmer of hope in the contest.
Ruben Selles's men thought they had found an unlikely equaliser just moments after when Theo Walcott chipped the ball past Steele to complete a fast break, however VAR spotted an offside in the build up.
Once again it was Ward Prowse at the centre of Southampton's positive play - the England international feed Walcott on the right, although the former Arsenal man had moved into an offside position before smartly cutting across Pervis Estupinan.
The Seagulls soon regained control of proceedings and made sure of a historic victory when Gross netted their third of the match after the Saints failed to clear their lines from a corner.
Estupinan delivered into the visitors' box, and the German midfielder picked up the loose ball before faking to shoot twice and firing an effort into the near post despite pressure from Joe Aribo.
Brighton have confirmed a top-seven finish in the Premier League and head into their final two matches of the campaign knowing only an unimaginable swing in goal difference will see them end up outside the Europa League places - Manchester City are next up for the Seagulls in midweek.
Southampton will look to avoid a sixth-straight defeat when they host Jurgen Klopp's Liverpool in the final game of their lengthy Premier League spell, with the Saints marching into the Championship in August for the first time since 2012.