An own goal from Brighton's Gary Hart and late finish from Burton O'Brien meant that the hosts, Crewe and Millwall were all relegated.
Wednesday took the lead when Hart deflected in Deon Burton's cross, and O'Brien sealed the win on 79 minutes.
Owls 'keeper Scott Carson kept the Seagulls at bay, while Dean Hammond was sent off for two bookable offences.
Sheffield Wednesday manager
"I'm delighted for everyone at the club.
"It's been a traumatic season, a rollercoaster, with injuries and players coming and going, but the last five or six weeks we have finally adapted to this league.
"We can grow from this, it will make us stronger, but we have to make sure we are not in a transitional period at the beginning of next season."
Brighton: Henderson, Hart, McShane, Butters (Hinshelwood 74), Lynch, Reid (Carole 56), Hammond, Carpenter, Mayo (Frutos 45), Noel-Williams, Kazim-Richards.
Subs Not Used: Martin, El-Abd.
Sent Off: Hammond (81).
Booked: Hammond, Lynch, Hart, Carpenter.
Sheff Wed: Carson, Bullen, Coughlan, Simek, Hills, Best (Brunt 72), Whelan, O'Brien, Adams, Tudgay, Burton.
Subs Not Used: McGovern, MacLean, Spurr, McAllister.
Goals: Hart 8 og, O'Brien 69.
Brighton are relegated
Ref: P Taylor (Hertfordshire).