The game had already seen four goals and a red card when Danny Pugh's heavy challenge on Inigo Calderon and subsequent booking sparked a furious reaction from the visiting bench.
In the ensuing bust-up, which involved players and staff from both benches, Owls boss Dave Jones was sent to the stands as stewards and police tried to restore order.
Brighton boss Gus Poyet kept his distance but was already staring down the barrel of a first league defeat in 2013.
On-loan duo Leroy Lita and Pugh both grabbed their first goals for the Owls and Ashley Barnes was given his marching orders for the visitors.
The Seagulls clawed a goal back through Andrea Orlandi but the hosts wrapped up the victory through Michail Antonio.
The hosts took the lead with just five minutes gone as Swansea loanee Lita acrobatically volleyed home from Antonio's cross.
Miguel Llera had to be alert to clear Calderon's teasing cross at the other end before a sloppy piece of play by Wayne Bridge afforded Antonio the freedom of the penalty area but his shot was wayward.
Brighton's task was made all the more difficult when Barnes was dismissed for kicking out at Kieran Lee after 33 minutes.
And from the consequent free-kick, on-loan Leeds midfielder Pugh found the bottom corner to compound the visitors' woes.
Poyet introduced Craig Mackail-Smith at the break in the hope he could add to his 11 goals this season.
It was the Owls who initially looked the more threatening in the second half, with Lita steering wide from inside the box.
Despite their numerical disadvantage, Brighton reduced the deficit after 54 minutes when Mackail-Smith pulled the ball back for Orlandi to convert.
But their joy was short-lived as within three 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 that Pugh was only given a yellow by referee Simon Hooper.
Order was finally restored but the riled visitors could not muster an unlikely comeback as their search for a first win at Hillsborough continued.
- Sports & Recreation
- Danny Pugh
- Inigo Calderon
- Leroy Lita
- Andrea Orlandi