James Harper was mobbed by delighted team-mates with his goal in the first minute of added time.
The win was a tonic for Reading, but they are still in danger of going down as the victims of second-season syndrome.
Middlesbrough had struggled to lift their game following the FA Cup extra-time win over Sheffield United in midweek.
Reading arrived at the Riverside low in confidence, but they battled away to deny the Teessiders any clear-cut scoring chances.
Manager Steve Coppell will hope this win gives his team lift-off in the desperate battle ahead.
Meanwhile, Boro boss Gareth Southgate will hope his team will raise their performance for the FA Cup sixth round tie against Cardiff City, particularly with a semi-final Wembley appearance at stake.
There was a lack of atmosphere at the start and this was reflected in the standard of play.
For the visitors, Shane Long headed over the bar and Stephen Hunt blasted high and wide in the early stages.
At the other end, England winger Stewart Downing shot straight at goal keeper Marcus Hahnemann from a pass by Afonso Alves.
Middlesbrough midfielder George Boateng was the first of several bookings by over fussy referee Howard Webb.
Hunt was an energetic presence for the visitors, but there was a lack of menace from either side and neither Hahnemann nor Mark Schwarzer were seriously tested before the break.
Reading kept a tight hold on Alves, although Middlesbrough's record £12million purchase looked short of match fitness.
The crowd tried to lift the home side after the break but there was scant response with a limited number of thrills at either end.
Both teams introduced substitutes in a bid to transform their fortunes without immediate effect.
Downing was among the bookings late in the game with the referee appearing to judge the local hero had taken a dive in what looked a harsh decision.
The game looked destined for a goalless draw long before the final whistle but Reading broke the deadlock in added time.
Hunt provided a cross from the left wing and Harper took advantage of a clear opening to beat Schwarzer.