The Millers opened the scoring after 26 minutes when Chris Sedgwick finished a superb run with an excellent finish past Kelvin Davies.
For a long period, the visitors had been looking at yet another defeat, however Jermaine Wright brought Joe Royle's men level with a 30-yard volley.
The East Anglian outfit suffered late on at home to The Baggies last week, but it was the promotion-hunting side who finished the stronger at Millmoor.
Darren Bent put the visitors ahead with just two minutes remaining when he latched onto Martijn Reuser's pass to finish easily.
With Rotherham going for broke, Town netted a third in injury time when Shefki Kuqi crashed home from the edge of the area to put them back in the play-off places.
Nationwide Division One
Rotherham United 1-3 Ipswich Town
