Goals from Neal Maupay and Danny Welbeck saw Graham Potter's side claim their fourth win of the campaign, before Jamie Vardy got one back in the second half.
A penalty decision from Stuart Atwell handed the home side the breakthrough they had been threatening throughout the first half.
A ball into the box was headed by Shane Duffy and struck Jannik Vestergaard at close range, with the referee pointing to the spot after a discussion with the assistant referee.
VAR then upheld the decision before Maupay sent Kasper Schmeichel the wrong way for his third goal of the season.
Brighton doubled their lead just after half-time, when former England international Danny Welbeck headed past Schmeichel.
The free-kick was put into the box from Leandro Trossard and Welbeck timed his run and jump well to nod into the back of the net.
Leicester pulled one back just after the hour mark, despite having looked behind the pace for much of the game.
Half-time substitute Ademola Lookman played a clever back-heeled one-two with Youri Tielemens who sent in a well-timed ball to the back post for Jamie Vardy to slot home for the 150th time for the club in all competitions.
The visitors appeared to have struck the equaliser when Lookman volleyed home, but it was ruled out.
The assistant referee had raised his flag for offside with VAR upholding the decision, with Harvey Barnes appearing offside as the ball came across the box and was judged to be in the line of sight of goalkeeper Robert Sanchez.
The Seagulls held on to win 2-1 and go up to third. It would have been second had it not been for a late winner for Manchester United against West Ham.