An unfortunate second-half own goal by Paul Hurst and Bobby Zamora's 11th of the season secured three precious points for Steve Coppell's side.
The fans, braving wind and rain, had little to warm them in a dull and untidy first half.
Brighton midfielder Richard Carpenter had a volley ruled out by a linesman because the ball had already crossed the line when Zamora crossed to him.
Seagulls captain Danny Cullip headed a Carpenter corner just wide, but defences were generally on top in a tough opening 45 minutes.
The home side achieved the breakthrough in fortunate circumstances in the 56th minute.
Tony Rougier, on loan from Reading, saw his close-range effort saved by Rotherham keeper Mike Pollitt but the ball rebounded off Hurst's face into the vacant net.
Zamora capitalised on Brighton's freak advantage by doubling the lead 11 minutes later.
He escaped unmarked from a Carpenter corner to slot in his fourth goal in six games at the far post.
Little was seen of Rotherham as an attacking force and they have now taken only one point from the last 12.
They only put veteran keeper Dave Beasant under pressure in the closing stages once manager Ronnie Moore had brought on Darren Garner and Richard Barker in a double change.
Beasant made a brilliant one-handed stop on the line from a close-range shot on the turn by Millers captain Martin McIntosh.
Former Seagulls forward Barker also headed against the bar from Garner's free kick, but it was too little too late for the Yorkshiremen.
Ronnie Moore accused his players of performing like a pub team. "It was one of our worst displays of the season," he moaned.