The Millers had gone in 2-0 up at the break, after a tepid first half burst into life with two goals inside four minutes.
Chances had been few and far between before Martin Butler notched his fifth goal of the season after 33 minutes by controlling the ball on the angle of the box and scooping it over keeper Paul Heald and into the far corner.
Heald was struggling with a knee injury suffered last week, but two minutes after the goal he prevented Rotherham from going further ahead with a superb save from a thumping Chris Swailes header.
But Swailes was not to be denied just two minutes later as John Mullin and Martin McIntosh combined to give the big defender a clear opening from six yards out and, even though Heald managed to get a hand to the ball, it looped into the far corner.
The brief barrage continued with Butler going close and then, when Heald was replaced by Lee Worgan, the newcomer almost had a nightmare start as a deep Richie Barker cross hit a post and bounced off his back and behind for a corner.
Rotherham made it 3-0 after 54 minutes, Carl Robinson's arching corner being met at the far post by skipper McIntosh, who glanced home a deft header, while 30 seconds later Butler ran clear and his 12-yard angled shot was tipped over by Worgan.
But the 19-year-old keeper was dramatically sent off after 63 minutes, when he charged out of his area and claimed the ball, meaning rookie Ben Harding took over in goal on his full Dons debut.
And the home side were also reduced to ten men when Stewart Talbot was sent off three minutes later for a second booking, after clattering Wayne Gray, and Adam Nowland rasped his 20-yard free-kick into the top corner to give the Dons at least some consolation.