A solitary strike from George Puscas was the difference as Rovers were undeservedly edged out by play-off chasing Reading at the Madejski Stadium.
Romanian frontman Puscas found the corner midway through the first-half to earn the points for the hosts.
After Harvey Elliott was robbed of the ball on the edge of his own box, ex-Rover Lucas Joao laid it on a plate for his strike partner to notch his fifth goal of the season.
That was the difference and it was extremely harsh on the visitors, who had dominated the encounter in Berkshire.
However, Rovers struggled to frequently test home goalkeeper Rafael Cabral despite having all of the possession against Veljko Paunovic's side.
The best opportunity fell the way of Ben Brereton, who stung the palms of Cabral in the second half, whilst Adam Armstrong later hooked inches past the post.
The result will no doubt be of real frustration for Tony Mowbray's charges, who did enough to draw the encounter at the very least due to an encouraging display.
Mowbray made three changes to his team at the Madejski Stadium with Barry Douglas, Jarrad Branthwaite and Lewis Travis dropping to the bench.
That meant there were recalls for Amari'i Bell, Taylor Harwood-Bellis and Tom Trybull, who all earned a spot in the starting team.
Reading worked a golden opportunity just three minutes in, but Puscas, who was the only change made by Paunovic, seeing his headed effort tipped over by Thomas Kaminski.
Rovers were settling into the game but were still to test Cabral, with Kaminski the busiest and called into action on 18 minutes to hold Alfa Semedo's curling attempt from range.
However, despite having the bulk of the possession, Rovers went behind soon after due to Puscas' precise finish.
Elliott was robbed of the ball on the edge of his own box, the ball fell kindly to Joao, and he fed the lurking Puscas, who slotted home.
With half-time looming, the in-form Brereton raced in from the left and saw his low strike held by Cabral as Rovers went in search of what would have been a deserved equaliser.
Michael Olise almost caught out Kaminski at his near post with a free-kick later on, but the Belgian held to ensure Rovers went into the interval a goal down, which was undeserved on the balance of play.
Rovers continued to dominate as the second half went on, but were maybe guilty of not testing Cabral enough.
It took until the 80th minute for Rovers to call the Brazilian into action, with the excellent Brereton forcing the stopper to beat away the drive, with the rampaging Ryan Nyambe prodding the ball wide from the follow up.
There was to be one final opportunity for Rovers in the final moments, but Armstrong could only divert just wide of Cabral's right post with an intelligent flick goalwards from a cross from the left.
That left Puscas as the match-winner, but Rovers will have found positives in a performance that saw them control the majority of the test, but one mistake proved to be costly on the night.
Reading: Rafael, Richards, Morrison (Holmes, 33), Moore (c), Olise (Esteves, 85), Ejaria, Yiadom, Joao (McIntyre, 69), Laurent, Semedo, Puscas.
Unused substitutes: Southwood, Baldock, Aluko, Tetek, Azeez, Camara.
Goal: Puscas, 24.
Booked: Semedo, 17.
Rovers: Kaminski, Nyambe, Lenihan (c), Harwood-Bellis, Bell (Douglas, 84), Evans (Downing, 61), Trybull (Buckley, 84), Rothwell (Dack, 61), Elliott (Dolan, 69), Armstrong, Brereton.
Unused substitutes: Pears, Travis, Branthwaite, Bennett.
Booked: Bell, 52, Evans, 58
Referee: Gavin Ward.