Martin Butler grabbed a brace, his first goals of the season, to ease the pressure on Millers boss Ronnie Moore.
The 29-year-old striker, signed from Reading for £150,000 following Alan Lee's departure earlier this season, struck in the 52nd minute and had a hand in Darren Byfield's 44th minute penalty before snatching a third in the last minute.
Stoke escaped in the seventh minute when they failed to cut out a Carl Robinson corner. Midfielder Julian Baudet powered in a close-range header but it was stopped on the line by Ed de Goey's oustretched leg.
The Frenchman then tested the Stoke keeper with a low strike that was smothered by the diving de Goey.
Carl Robinson curled a free-kick over the bar before Rotherham almost snatched the lead on 22 minutes. Robinson's corner reached centre back Martin McIntosh whose crisp header was hacked off the line by Karl Henry.
Stoke then caught the Millers on the break and lanky striker Chris Iwelumo hit the bar after connecting with a Darel Russell centre .
Busy midfielder Kris Commons then pulled his 16-yard shot wide.
Byfield should have put Rotherham ahead five minutes before the interval after running onto a Paul Warne cross but from 15 yards he shot straight into the arms of de Goey before slotting home his spot kick a minute before the interval.
Baudet went close with a low strike before Rotherham grabbed a second, Wayne Thomas blundered as he tried to clear and Butler stabbed the ball home from close range.
Butler had a header from six yards cut out by de Goey and defender Chris Swailes saw his header fly narrowly wide before Butler grabbed Rotherham's third seconds from time stabbing in a Byfield cross.