Jon McLaughlin made several smart stops before Chris O'Grady tapped in against his old club to put the Brewers ahead.
The Millers had been on top but fell further behind when John Brayford crossed for Jackson Irvine to head in.
Tom Adeyemi reacted fastest to a save to pull one back, but Rotherham lacked the quality to find an equaliser.
Relive Burton's victory at Rotherham as is happened
Defeat leaves the Yorkshire side, led by caretaker-boss Paul Warne, 10 points from safety, while Burton move up two places to 19th.
It was a first away triumph of the season for Nigel Clough's side while O'Grady's goal was his first in 389 days, as he was on hand to score after Lewis Price spilled a shot.
Burton full-back Brayford spent several minutes being treated after a head injury, but came back on to assist Irvine before being replaced at the interval.
Rotherham were chasing back-to-back Championship wins for the first time this season, but they have now conceded 52 league goals.
Darnell Fisher volleyed wide and Izzy Brown could not find the target from inside the area as the hosts pressed, in vain, for a point.
Burton manager Nigel Clough: "We didn't play anywhere near as well as we did at Aston Villa on Boxing Day but we battled away for three points.
"It was tough coming here, we knew that they would have their tails up. We knew they would come out and cause us problems and they did.
"The only disappointment was that we conceded just before half-time and that gave them a chance, they put us under a lot of pressure in the second half.
"The timing in the year we didn't want to go into the new year without an away win. It is important psychologically to not be in the bottom three going into the new year."
Rotherham's caretaker boss Paul Warne: "We played really well. We were the better team and, with respect to Burton, I thought they came for a point.
"I love my lads but with the greatest of respect to them, they aren't used to playing against and having to break down two banks of four.
"Did they underachieve in the scoreline? Yes. But did they underachieve in the performance? No, I don't think they did.
"They are devastated, it will be tough to pick them up. But I don't believe we are relegated, I still think we have got a chance.
"If I didn't then I would tell the chairman to get a different caretaker in."
Match ends, Rotherham United 1, Burton Albion 2.
Darnell Fisher (Rotherham United) is shown the yellow card.
Second Half ends, Rotherham United 1, Burton Albion 2.
Corner,  Rotherham United. Conceded by Tom Flanagan.
Foul by Isaiah Brown (Rotherham United).
Lucas Akins (Burton Albion) wins a free kick in the defensive half.
Shaun Barker (Burton Albion) is shown the yellow card for a bad foul.
Lee Frecklington (Rotherham United) wins a free kick on the left wing.
Foul by Shaun Barker (Burton Albion).
Substitution, Burton Albion. Shaun Barker replaces Matthew Palmer.
Delay over. They are ready to continue.
Delay in match Lucas Akins (Burton Albion) because of an injury.
Foul by Peter Odemwingie (Rotherham United).
Lucas Akins (Burton Albion) wins a free kick in the defensive half.
Danny Ward (Rotherham United) is shown the yellow card for a bad foul.
Corner,  Rotherham United. Conceded by Tom Flanagan.
Attempt saved. Peter Odemwingie (Rotherham United) right footed shot from outside the box is saved in the bottom right corner.
Substitution, Rotherham United. Dexter Blackstock replaces Joe Mattock.
Darnell Fisher (Rotherham United) wins a free kick in the attacking half.
Foul by Tom Naylor (Burton Albion).
Offside, Burton Albion. Lloyd Dyer tries a through ball, but Lucas Akins is caught offside.
Foul by Aimen Belaid (Rotherham United).
Marcus Myers-Harness (Burton Albion) wins a free kick on the right wing.
Attempt missed. Lee Frecklington (Rotherham United) right footed shot from outside the box misses to the left.
Substitution, Rotherham United. Greg Halford replaces Tom Adeyemi.
Attempt missed. Isaiah Brown (Rotherham United) right footed shot from the left side of the box misses to the right. Assisted by Peter Odemwingie.
Corner,  Rotherham United. Conceded by Damien McCrory.
Damien McCrory (Burton Albion) is shown the yellow card for a bad foul.
Peter Odemwingie (Rotherham United) wins a free kick on the right wing.
Foul by Damien McCrory (Burton Albion).
Joe Newell (Rotherham United) wins a free kick in the defensive half.
Foul by Lucas Akins (Burton Albion).
Attempt saved. Peter Odemwingie (Rotherham United) left footed shot from outside the box is saved in the centre of the goal. Assisted by Lee Frecklington.
Matthew Palmer (Burton Albion) is shown the yellow card.
Foul by Lee Frecklington (Rotherham United).
Lucas Akins (Burton Albion) wins a free kick in the attacking half.
Corner,  Burton Albion. Conceded by Joe Mattock.
Offside, Rotherham United. Aimen Belaid tries a through ball, but Peter Odemwingie is caught offside.
Substitution, Burton Albion. Marcus Myers-Harness replaces Chris O'Grady.
Attempt missed. Darnell Fisher (Rotherham United) right footed shot from the right side of the box is high and wide to the right.
Two quick first-half goals helped Burton edge past bottom side Rotherham and move five points clear of the Championship relegation zone.