The England Under-21 left-back struck eight minutes from time to give Mark McGhee's strugglers their seventh 1-0 win of the Championship season.
A free-kick by Darren Currie flicked off the head of a Rotherham player to Harding at the far post and he drilled a low shot past keeper Mike Pollitt.
Pollitt had earlier kept Rotherham on level terms with some significant saves.
Early on he smothered an effort from Steve Claridge, after recalled striker Leon Knight had put the veteran through.
Pollitt then held Claridge's glancing header from Knight's cross and parried a long-range effort by Currie as Brighton had the better of the first half.
It was the same story after the break and Knight flashed an effort wide of the near post following a cross-field pass by Paul Reid.
Knight then latched on to a flick by Claridge and managed to beat Pollitt to the ball, only for Rotherham captain Martin McIntosh to clear off the line.
Brighton looked like being frustrated when Knight dragged a shot wide of the far post from Reid's quickly taken free-kick, but Harding finally pounced to secure only their second win in seven matches.
Rotherham, still without an away win this season, rarely looked like building on their first victory of the campaign at home to Leeds on Monday. They offered little as an attacking force and look doomed to relegation.