Alex Revell headed the only goal of the game in the 76th minute to seal a first win in four games for the Millers and inflict only the Dons' second defeat in six, with their recent form having put valuable distance between themselves and the League Two drop zone.
All the first half attacking came from Rotherham but they could not find a way through the massed ranks of visiting defenders.
Twice Dons goalkeeper John Sullivan pulled off good saves to thwart the hosts, whose wayward finishing also let them down. Sullivan saved well from Claude Davis after 24 minutes and then pulled off an even better stop to deny Lee Frecklington.
Johnny Mullins shot over from just six yards out, Frecklington lifted another shot over the bar and both Revell and Kari Arnason headed wide as the Millers continued to push.
Wimbledon waited until the 43rd minute before managing an effort on goal, with Alan Bennett heading wide from Mat Mitchel-King's cross.
Five minutes after the break Danny Kearns shot just wide and then he provided the cross from which Mullins should have put Rotherham in front, but from six yards out he headed over the bar.
At the other end Harry Pell produced a terrific shot which Scott Shearer tipped over the bar.
But the breakthrough finally came in the 76th minute from substitute Lionel Ainsworth's corner, Arnason flicked on at the near post and Revell headed home.