Rooney opened the scoring by slotting home from a Dave Brammer corner, then met Josip Skoko's pass for his second.
Mamady Sidibe's drilled shot from a Rooney pass made it 3-0 and Sidibe returned the favour to allow Rooney to score his third goal from eight yards.
Substitute Peter Sweeney added a fifth before Doug Loft grabbed a late consolation for the Seagulls.
Stoke boss Johan Boskamp on leaving the club:
"I'm not sad, but disappointed to leave but football goes on and I think Stoke have a great future.
"It's not bad to finish with a 5-1 win, and I hope our good following of fans enjoyed it. We've made progress, winning 10 games away from home.
"I believe if the team is kept together things will develop well."
Brighton: Henderson, Reid, Hinshelwood, Butters, Lynch, Nicolas, Carpenter, Carole, Frutos (Loft 58), Noel-Williams, Kazim-Richards.
Subs Not Used: Chaigneau, Mayo, El-Abd, Gatting.
Goals: Loft 84.
Stoke: Simonsen, Duberry, Hill, Mbuyi, Buxton, Brammer (Garrett 70), Russell, Skoko (Kopteff 83), Dickinson, Rooney (Sweeney 77), Sidibe.
Subs Not Used: de Goey, Broomes.
Goals: Rooney 6, 22, Sidibe 40, Rooney 63, Sweeney 82.
Ref: K Wright (Cambridgeshire).
Play-off semi-final dates:
Leeds v Preston
(Elland Road, Friday, 5 May, 1945 BST)
Crystal Palace v Watford
(Selhurst Park, Saturday, 6 May, 1215 BST)
Preston v Leeds
(Deepdale, Monday, 8 May, 1945 BST)
Watford v Crystal Palace
(Vicarage Road, Tuesday 9 May, 1945 BST)
Play-off dates for other divisions to be confirmed