Patrick Bamford put Leeds ahead in controversial circumstances at Elland Road with heavy suggestions of handball after a deflected cross appeared to brush his arm on its way in.
Crysencio Summerville added a second after the break for the dominant Whites and later scored his second from the penalty spot as the hosts made it six Championship wins in succession.
Leeds were aiming to maintain their unbeaten start to 2024 while Rotherham, the Championship's basement club, were seeking their first win since Boxing Day.
Daniel Farke made six changes from the Leeds side that beat Plymouth in midweek FA Cup action and opposite number Leam Richardson named an unchanged team from that which tasted defeat to Southampton last weekend.
After early Rotherham pressure, Wilfried Gnonto got in behind the Millers but was unable to find Summerville ahead of goalkeeper Viktor Johansson.
Georginio Rutter's promising cross then found Bamford but his weak effort was claimed by Johansson after five minutes.
Bamford was denied before 10 minutes was played by Hakeem Odoffin's low tackle after Rutter's good work as the hosts continued to apply pressure.
Leeds took the lead when Junior Firpo's left-wing cross deflected off Rotherham skipper Sean Morrison and struck what appeared to be Bamford's arm to put the Whites ahead.
Rutter's shot from outside the box flew just over before Summerville wasted a glorious chance after Firpo robbed Odoffin and the winger blasted his 25th-minute effort over, with Rutter being denied by Johansson moments later.
Ethan Ampadu's fantastic long pass put Bamford through one-on-one but he was unable to control it 10 minutes from half-time.
Archie Gray nearly capped off a sustained Leeds move but fired straight at Johansson before the stopper denied Gnonto's fiercely-struck effort just before the break to keep the deficit at just one.
Illan Meslier was sharp to control Glen Kamara's back pass and prevent an own goal early in the second half.
Leeds should have doubled their lead when Bamford struck the bar and Gnonto blasted a follow-up over from close range.
But Summerville gave Leeds a deserved second as he exchanged passes with Rutter and buried past an onrushing Johansson after 52 minutes.
Referee Andrew Madley pointed to the penalty spot when Peter Kioso brought down Summerville and the winger coolly converted on the hour mark.
Gnonto could have made it four but his low 78th-minute drive fizzed inches wide before a rare Millers foray forward saw Christ Tiehi blast over following a corner.
Johansson collected Rutter's header as full-time approached before Meslier denied Odoffin's header at the other end, with Rutter blasting inches wide in stoppage time.