Ben Pringle's goal earned the Millers victory shortly after the restart when he converted from close range.
The home side had an early shout for a penalty waved away when Marc Beevers went down under a challenge inside the box.
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Pringle grabbed the winner four minutes after the restart when he tapped home, before Ricardo Fuller saw a header deflected narrowly wide on 65 minutes.
Ian Holloway made a couple of late changes, but he was unable to inspire a change as the Millers held on for the win.