Caretaker manager Neil Redfearn suffered his first defeat in his first home game since taking over from Simon Grayson.
The game sprung to life in the final fifteen minutes of the game. Craig Mackail Smith fired the visitors ahead.
Luciano Becchio quickly equalised for Leeds but a goal by Alan Navarro in stoppage time won the game for the visitors.
Becchio had a good early chance but he headed wide from close range.
Leeds had strong penalty claims waved away by referee Graham Salisbury when Adam El-Abd brought down Ross McCormack inside the area.
Moments later Tom Lees headed over from a Robert Snodgrass free kick.
McCormack then saw an effort go harmlessly wide as neither side could find the target in the opening twenty minutes.
Brighton started to come into the game and Alan Navarro had the first effort on target but his shot was straight at Andy Lonergan in the Leeds goal.
The visitors were enjoying a good spell and Kazenga Lua Lua fired wide.
Liam Bridcutt then saw a long-range effort parried away by Lonergan.
After a good start to the game by Leeds but without ever testing the Brighton keeper, the visitors came back into the game with the half closing with both sides nullifying each other.
Leeds had a decent chance at the start of the second half when Brezovan spilled a cross from Snodgrass and the ball was eventually scrambled out for a corner.
From the corner, Adam Clayton fired wide.
Brighton responded and Joe Mattock saw a shot deflected for a corner.
From the corner, Lonergan made a great save to deny Sam Vokes and minutes later, a scrambled clearance off the line from Leeds kept the game goalless.
The game was much more open in the second half. Adam Smith fired well over for Leeds after good work from Snodgrass.
McCormack then found himself in behind the Brighton defence but he shot well over.
McCormack then saw a free kick take a deflection and out for a corner.
The game was beginning to get scrappy with Brighton starting to waste time and Becchio and Snodgrass going into the referee`s notebook in quick succession.
Brighton took the lead in the final fifteen minutes when Mackail-Smith who had only been on the pitch a matter of minutes headed home.
Leeds were quickly back on level terms when Becchio headed home following a Snodgrass corner.
Brighton retook the lead in injury time when Alan Navarro fired home from the edge of the area.
It was to prove the last chance of the game as Brighton recorded only their second ever win at Elland Road.
Lonergan, Smith, Lees, O`Dea, White (Townsend 81), Snodgrass, Clayton, Delph, Pugh, McCormack (Nunez 90), Becchio
Subs not used
Taylor, Bruce, Brown
Brezovan, El-Abd, Greer, Bridcutt, Buckley (Noone 46), Jara, Navarro, Mattock, Lua Lua (Vicente 61), Vokes (Mackail-Smith 73), Barnes,
Subs not used
“Neil Redfearn is a good coach. He has played over 1000th games for a load of different clubs and at this level and higher. He is experienced, knowledgeable and a good coach.
“Things have definitely changed on the training ground big time since he has been in charge. It is more organised and he is preparing players for a system to work to a system.
“When you are a youth team coach at a club you are teaching kids and when you move up to the first team, the bigheads need to respond to you. If the bigheads respond to him, as they have so far, he will be ok.
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