Time is running out for Brighton manager Martin Hinshelwood, after his side slumped to their eighth defeat in a row.
The defeat came as Rotherham continued their unbeaten home run at Millmoor with a controversial first half goal from Alan Lee.
Early on Rotherham, eager to cash in after their win at Walsall on Tuesday, were lively as Brighton looked nervy at the back after seven defeats in a row.
A Chris Sedgwick cross from the right had the visitors' defence in trouble, but Lee's tame header was straight at keeper Andy Petterson.
Brighton looked good after 11 minutes, breaking forward smartly. John Piercy drilled a low cross from the right but Gary Hart smashed his first time shot over.
But Rotherham controversially went ahead after 20 minutes. Darren Byfield burst forward and was tackled by Charlie Oatway.
The ball broke to Lee who was clearly offside, but referee Mike Pike waved play on despite a linesman's flag when the ball broke off the Brighton player.
As the Brighton defence stood rooted and the keeper strolled off his line Lee finished with a casual lob from 35 yards, sparking furious protests from the Brighton camp as the referee gave the goal.
Rotherham should have stretched their lead before the break, but Byfield shot wide and Chris Swailes was off target.
Rotherham went off the boil after the break as Brighton shackled Sedgwick. In a rare attack it was Sedgwick who broke inside but blazed his 20-yard effort wide.
Brighton came close to an equaliser in the 60th minute when Hart pounced with a sharp volley but Mike Pollitt turned it away for a corner. And when Daniel Marney went on an impressive run Rob Scott had to produce a timely challenge