Substitute Alan Lee was the hero for Dave Jones' side with the winner just moments after replacing Michael Ricketts.
Lee struck with his first touch 16 minutes from time, latching on to a pass by Joe Ledley to strike the 50th league goal of his career from close range.
Brighton must be sick of the sight of Lee. He also scored a controversial winner against them for Rotherham three seasons ago.
Cardiff could have been out of sight by half-time after Jason Koumas had given them a 12th minute lead.
Cameron Jerome, fresh from his England under-21 call-up, did the donkey work with a powerful run which took him away from Brighton defenders Gary Hart and Paul McShane.
Jerome then squared the ball across the face of the area for Koumas, on loan from West Brom, to score with a precise shot into the roof of the net from 16 yards.
Koumas, Jerome and Kevin Cooper all came close to extending Cardiff's lead in the opening 45 minutes.
Brighton's solitary response was a glancing header just wide off the target by McShane from Hart's cross.
Jerome, causing the Brighton defence all sorts of problems, set up a great chance for Ledley early in the second half after outmuscling McShane, but Paul Reid made a last-gasp block.
That looked like a turning point as Brighton levelled three minutes later.
A clever pass by Dean Hammond released Jake Robinson inside the Cardiff area. His shot was parried by Neil Alexander for McShane to tuck in his second goal in four games from point-blank range.
The game could have gone either way at that stage before Lee made sure it went the way of the visitors.
Ricketts, earlier booked after appearing to tread on McShane, was replaced by the big front man.
Within seconds Lee capitalized on slack defending by Brighton to score his first goal since January.