AFC Wimbledon were made to pay for missed chances as Sam Wood scored the only goal late in the second half to give Rotherham all three points.
Luke Moore should have put the visitors ahead inside the first minute but shot well over, while Seb Brown twice denied Rotherham's Danny Harrison.
Moore, Lee Minshull and Jack Midson all missed further chances for Wimbledon.
The only goal came 12 minutes from time when Lewis Grabban pulled the ball back to Wood, who fired in off the post.
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Rotherham boss Andy Scott told BBC Radio Sheffield:
"I'm pleased with the result, I'm pleased with the clean sheet. How we got it I don't know to be honest but we got it and probably this is the first time this season where we can say we've had a bit of luck on our side.
"It wasn't a great game, I don't think either side really got any momentum going. It was a funny sort of game, we had a couple of chances early on and then they had a couple of chances and then it died a little bit. No one could really get a foothold.
"We didn't put the ball into our front players feet when there was plenty of space. It's things we worked on this week and it's so frustrating seeing it open up in the game and we didn't execute it properly."
AFC Wimbledon manager Terry Brown told BBC London 94.9:
"I'm absolutely distraught because we needed a win today for morale and to get points to lift us up that table.
"It was a really impressive performance. We've come to a difficult stadium, we were playing a good side and I thought we had the majority of the match.
"I have to take the positives out of the performance. We were solid, resilient and difficult to beat."