Pablo Counago's second-half brace sealed Ipswich's fourth win in five league games after a stormy encounter at Portman Road.
Visitors Rotherham lost their heads after Counago netted a controversial penalty and ended with nine men after both Martin MacIntosh and Julian Baudet were sent off.
The first half was a miserable affair, with neither side looking likely to score, and showing why they began the day in the bottom half of the table.
Thankfully the second half was much more lively, with only a fine Kelvin Davis save denying Martin Butler two minutes after the break.
George Santos shot wide for Town before Counago opened the scoring on 53 minutes, flicking in Jim Magilton's corner.
A heavy touch by Shefki Kuqi after Allan Mahon put him through lost one chance and then referee Andy D'Urso failed to award a penalty after a tackle from behind on Counago by Chris Swailes.
Rotherham levelled on 59 minutes when Butler glanced a header beyond Davis after Paul Warne's initial shot.
Mike Pollitt saved Counago's close-range volley from a Kuqi header before Darren Byfield sent an overhead kick narrowly wide.
Town regained the lead on 70 minutes with a Counago penalty, given despite an apparently clean challenge by Chris Sedgwick on Chris Bart-Williams.
Magilton blazed over from a Counago pass before MacIntosh was sent off for his second bookable offence, bringing down the Spaniard on the edge of the box.
D'Uso angered Rotherham again when he failed to award them a penalty after Santos appeared to trip Byfield.
The visitors had a second man sent off five minutes from time, when Baudet reacted to a late challenge by Mahon, by grabbing him around the throat, giving the referee no option.
Ipswich held on comfortably after that, but the visitors will leave Suffolk feeling aggrieved at how the two controversial penalty incidents, one given and one declined, went in the second half.