To make matters worse for Kevin Blackwell's men, they had captain Paul Butler and England U-21 defender Matthew Kilgallon sent off in the closing stages.
Former QPR defender Carlisle diverted the ball past his own keeper Neil Sullivan as Brighton centre-forward Adam Virgo challenged him from a free-kick by Darren Currie.
Leeds created the first real chance when midfielder Frazer Richardson let loose with a left-footed shot from 20-yards which was comfortably collected by Michel Kuipers.
Both sides had players booked in a two-minute spell in which United full-back Gary Kelly was cautioned for showing dissent.
Minutes later Brighton midfielder Richard Carpenter, one of two changes to the side that drew 1-1 with Cardiff on Tuesday, was the shown a yellow card for a foul on Michael Ricketts.
Dean Hammond then forced Sullivan into a save from close range.
Sullivan then kept out a Leon Knight shot six minutes before the break, but it was Currie who should have put The Seagulls in front two minutes later when he shot wide with the goal at his mercy when a mistake by Kelly put him clean through.
After the break United substitute Brian Deane, on for Michael Ricketts at half-time, went close when he rose above the defence only for his header to miss the right-hand post.
Simon Walton, who became the fourth Leeds player to go into Richard Beeby's book, fired over the bar before he was taken off for midfielder Matthew Spring 20 minutes from time.
Leeds then replaced Richardson with Aaron Lennon at the same time only moments before Knight missed the chance to double Brighton's lead with a header which just flashed wide.
Leeds, punchless once again up front, shot themselves in the foot twice as they searched for an equaliser.
Kilgallon had already been booked in the 49th minute for a foul on Brighton midfielder Charlie Oatway when he tackled substitute Gary Hart from behind in the 87th minute.
The referee produced a second yellow card for United's young left-back, and things got even worse for them deep into stoppage time.
Butler had only just been booked for dissent when the official showed him a straight red card as Brighton prepared to take a corner.
Mr Beeby later revealed Butler had been sent off for foul, abusive and insulting language.
Brett Ormerod, making the last appearance of his loan spell from Southampton, came closest to helping The Whites avoid their first defeat in five games.
His angled 75th minute drive from a cross by Lennon flashed just wide of the far post.
Oatway joined Brighton's lengthening injury list. He was eventually forced off in the second half by a foot problem sustained in the tackle which resulted in Kilgallon's first caution.