Sheffield Wednesday got their sixth win in nine Championship matches to inflict Brighton's first league defeat of 2013.
Leroy Lita put the Owls ahead early on, before Brighton's Ashley Barnes was sent off for kicking Kieran Lee.
Danny Pugh then put Wednesday 2-0 up and, although Andrea Orlandi pulled one back after the break, Michail Antonio wrapped up the victory for the hosts.
The game was marred by a late fracas involving players and staff from both benches sparked by a Pugh foul.
His heavy challenge on Inigo Calderon and subsequent booking sparked a furious reaction from the visiting bench and Owls boss Dave Jones was sent to the stands as stewards and police tried to restore order.
The hosts took the lead with just five minutes gone as Swansea loanee Lita acrobatically volleyed home from Antonio's cross.
Brighton's task was made all the more difficult when Barnes was dismissed and from the the subsequent free-kick, on-loan Leeds midfielder Pugh found the bottom corner.
Despite their numerical disadvantage, Brighton reduced the deficit after 54 minutes when Craig Mackail-Smith pulled back for Orlandi to convert.
But their joy was short-lived as within two minutes Antonio restored Wednesday's advantage with a scrappy close-range finish for his seventh goal of the season.
Pugh's foul on Calderon after 70 minutes preceded a lengthy stoppage in play as the away bench demonstrated their anger at the fact Pugh had only been given a yellow by referee Simon Hooper.
Brighton manager Gus Poyet on the red card:
"In football sometimes you do things that you regret after, but [I have] nothing to complain about.
"I think you would normally probably say you're not happy with him [Barnes].
"Angry? It's difficult to say because I played football, I know when you're on the pitch you do things which sometimes you regret after but I was one of those players so I'm not going to say anything to Ashley Barnes - I hope it doesn't happen too much."
Sheffield Wednesday manager Dave Jones:
"Things happen within a game. The sending-off was pivotal in it as well - and deservedly so, the lad stamped on him.
"Then I just felt every challenge we made, they [Brighton] were trying to even it up and I didn't think that was right and that's what the fracas was over. It's handbags at the end of the day, it's done and dusted now, it's over.
"I think the referee did the right thing just to calm it all down because it would have just carried on. I'll see what he puts in his report and if he gets it right."