Defeat consigned the Millers to a fifth-straight loss and they remain deep in relegation trouble after conceding midway through the first half to Michael Morrison.
Reading's own form has faltered in recent weeks with just one win in six before this, but their play-off bid got back on course with this slender victory.
Rotherham had the first opening with Michael Smith heading the ball over from Lewis Wing's free-kick.
Home goalkeeper Viktor Johansson had to make a smart stop at the other end after Omar Richards volleyed through a crowd of bodies.
The injury-hit Millers were dealt another blow when Clark Robertson limped off injured but they almost took the lead from the next play when Freddie Ladapo headed off target from Smith's hooked pass.
Reading took the lead in the 26th minute with a scrappy goal as Morrison managed to force the ball over the line at the second time of asking from Richards' cross.
The visitors should have been celebrating again when Liam Moore found acres of space and crossed for Lucas Joao but the Portugal international could only bundle an effort wide.
Ladapo again skewed off target after he latched on to Angus MacDonald's flicked header.
Alfa Semedo should have doubled Reading's lead before the break as an Ovie Ejaria free-kick bobbled through to him and seemingly took him by surprise as he poked the ball wide from close range.
Rotherham made a bright start to the second half with Ladapo heading over the top from Matt Crooks' cross.
A scrappy second half was suiting Reading, who looked to catch Rotherham on the counter, dangerman Joao led one attack but he made a mess of a chipped effort after breaking clear.
The ball fell kindly to Rotherham loanee Wing at the edge of the box but he skied the ball high and wide.
The home side were largely being restricted to efforts from distance and Smith was the next to take aim, but again could not trouble Reading goalkeeper Rafael Cabral.
Michael Olise also tried his luck from well outside the box but his volley bounced wide of Johansson's goal and he then drove straight at the Swedish stopper from similar range.
Rotherham substitute Trevor Clarke made good contact with a shot from the edge of the box but it was easily gathered by Cabral.
The away side had to endure a nervy five minutes of injury time with Ben Wiles' deflected effort drifting just inches wide of the post but they held on for maximum points.