In a game of very few chances Mark Wright settled the game with a breakaway goal in the 82nd minute.
The victory stretches the Dons' unbeaten run to eight games while Rotherham suffered only their second loss in 16 matches.
Rotherham started the brighter with Marc Joseph blazing over the top after seven minutes and Derek Holmes heading the first of a number of chances that fell his way off target.
Jordan Hadfield had what proved to the Dons' only chance of the first half on 12 minutes when his 20-yard drive was diverted wide by team-mate Colin Cameron.
Ian Ross found Holmes with a deep cross but again the Rotherham striker headed wide, as he did on 36 minutes from another Joseph cross.
Rotherham continued to press in the second half but were finding it hard to break down the visitors' 4-5-1 formation.
Chris O'Grady lobbed over the crossbar on 52 minutes as the Dons restricted the hosts to long-range efforts.
The best chance to fall to Mark Robins' side went to Holmes on 64 minutes from Stephen Brogan's free-kick, but the Scotsman's point-blank header was saved by the feet of goalkeeper Willy Gueret.
Mark Hudson and Ryan Taylor both had long-range shots for Rotherham before, in the 82nd minute, the Dons, who have lost only once away from home, struck the decisive blow.
A Rotherham free-kick on the right broke down when Joseph lost possession inside the Dons half and Jemal Johnson burst forward. He beat Ian Sharps and laid the ball off to Wright who slid the ball under Andy Warrington.