The second-half goal by Ryan Williams was his first of the season and came in his 32nd appearance
Defender Semi Ajayi scored twice as Rotherham ended a run of five consecutive draws to dent out-of-form Blackburn's fading play-off chances.
The Nigerian's first came inside two minutes when he headed home a trademark long throw by Will Vaulks.
Rovers, who have now lost five of their past six matches, levelled through Amari'i Bell's close-range strike.
But Ryan Williams poked in to make it 2-1 and Ajayi powered in his third goal in three games from a Vaulks cross.
Charlie Mulgrew's emphatic penalty in injury-time brought hope for the visitors, however Rotherham held on for a victory which would have taken them out of the relegation but for Reading's dramatic late win over Ipswich.
Rotherham, who had failed to win any of their past four home league matches, caused Rovers problems from set-pieces throughout.
After Ajayi's early effort, Jon Taylor and Richard Towell went close from long throws, while Vaulks shot wide from a tight angle.
Bell's simple finish following a Mulgrew free-kick drew Rovers level as they improved after the break in an increasingly open match.
But midfielder Williams and Ajayi ensured victory despite Mulgrew's 93rd-minute spot-kick, after Michael Ihiekwe fouled Danny Graham, causing a few late concerns.
Rovers drop to 17th, 10 points off the play-off places and 11 above the relegation zone while the Millers remain in the bottom three on goal difference.
Rotherham manager Paul Warne:
"We were a bit nervy and it sounds a stupid thing to say, but I think we scored too early.
"I have been critical of the team for not taking chances, but we took 100% of our chances.
"Overall I am really proud of the points and the lads for digging in. All we can do is try and win and it looks like we have pulled other teams into it. We don't make it easy, but we are good value for money."
Blackburn boss Tony Mowbray:
"We are obviously disappointed. It's a common theme now - if you can't keep clean sheets you are not going to win games.There were a lot of positives, but the negatives are there right in front of our face.
"We came out of League One, like Rotherham. You have to improve and get better, we have to do the same.
"It's football, if you stand still, you're going backwards. So we will resolve the problems in front of us when we get the opportunity."
