An even first half, high on endeavour yet low on quality, only sparked to life when Middlesbrough goalkeeper Joe Lumley made a sprawling save to deny home top scorer John Swift.
But Swift set up what proved to be the Reading winner in the 55th minute, with Alen Halilovic somewhat fortuitously guiding home from the cross for his first goal for the club.
Middlesbrough’s frantic search for a late equaliser was not helped when forward Matt Crooks was sent off in the 86th minute after clashing with home goalkeeper Luke Southwood.
Reading had taken seven points from their previous three games, including a 2-1 victory at Fulham last Saturday.
But reports in midweek claimed that they faced a deduction of up to nine points for alleged breaches of the EFL’s financial guidelines. The Berkshire club have yet to make an official comment on the issue.
Middlesbrough had won only two of their opening eight league matches, including just one of their past six.
Injury-hit Reading, without 10 first-team players, fielded a bizarre outfield line-up featuring two defenders and eight midfielders or wingers.
Josh Laurent, a midfielder, and Andy Yiadom, a full-back, stood in as emergency central defenders – with none of Reading’s five senior centre-backs available.
In a cagey opening, neither side managed to create much going forward.
Middlesbrough momentarily thought that they had gone ahead in the third minute, when Crooks nodded in from an Isaiah Jones cross.
But the ball had been taken over the byline by Jones before his cross and Crooks’ effort was quickly disallowed.
Reading replied decisively and, after Ovie Ejaria had a shot blocked, Halilovic found Swift in space inside the Middlesbrough area.
Swift had only Lumley to beat but he shot too soon and the keeper did well to deny him his eighth goal of the season.
Middlesbrough threatened only sporadically but, when striker Andraz Sporar did manage to wriggle free of attention, he fired wildly wide.
Reading made the more promising start to the second half, with Chelsea loanee Danny Drinkwater releasing Tom Dele-Bashiru with a superb pass.
But Dele-Bashiru’s finish was poorly directed and Lumley saved with his right foot.
Reading, though, finally managed the breakthrough 10 minutes after the break – with a touch of fortune.
A good cross from Swift saw Halilovic totally miscue his attempt, thereby wrongfooting Lumley and allowing the ball to trickle into the empty net.
Middlesbrough worked hard for the equaliser but Crooks saw red four minutes from the end when lunging at Southwood as the keeper tried to gather a loose ball in the home area.