In a contest of few clear-cut openings, Boro skipper George Friend settled the issue with a smartly taken goal in the 77th minute.
Reading competed vigorously throughout but could not take advantage of the several half-chances that came their way.
Boro had not won in their past five matches in all competitions and lost 1-0 at home to League One Burton in their Carabao Cup quarter-final on Tuesday.
Manager Tony Pulis made six changes to the starting XI that faced Burton for the trip to the Madejski Stadium.
Reading had not won in their past six outings, though had drawn four of them.
Caretaker manager Scott Marshall took charge for his third game, which was expected to be his last.
Reading were hoping to appoint Jose Gomes, the Portuguese coach of Primeira Liga club Rio Ave, as their new boss this weekend.
Boro made a sluggish start and were almost breached in the early exchanges.
Sam Baldock was able to wriggle clear inside the area but his fierce shot was kept out by goalkeeper Darren Randolph.
Boro were quick to recover and launched a series of attacks.
Centre-back Aden Flint headed wide from an Adam Clayton cross and Ryan Shotton fired wide from an angle.
Britt Assombalonga was then denied when home keeper Anssi Jaakkola got down well to block the Boro striker's close-range effort.
The visitors thought that they had gone in front, when Shotton nodded in following a free-kick, but the goal was quickly ruled out for offside.
Having held firm at the back, Reading improved going forward before the break.
But on-target attempts from Danny Loader and Omar Richards were both saved by Randolph.
Reading were the first to threaten after the interval through captain Leandro Bacuna.
He cut in cleverly from the left only to see his shot take a slight deflection, which allowed Randolph to gather easily.
Boro replied from a George Saville corner, which found the unmarked Flint at the far post.
Flint, however, was unable to muster any power with his header and Jaakkola also gathered comfortably.
Reading responded with a swift counter-attack, with Loader releasing Baldock.
But as the forward prepared to shoot, he was crowded out by the retreating defence.
Boro finally made the breakthrough with 13 minutes left, when substitute Paddy McNair weaved his way to the right-hand byline.
His cross was driven in low and hard, with Friend arriving at the right moment to slam home from six yards out.
Friend almost added a second in the dying stages but sliced a shot on to the home crossbar after a goalmouth scramble.