Craig Hignett scored in the 89th minute last night to break the deadlock and deny Reading, who had famously won at Leeds in the previous round, a place in the semi-finals of the League Cup for the first time in their history.
It was tough on Reading, who were missing four key defenders with injury yet gave a good account of themselves against the First Division leaders.
Reading twice went close to taking the lead in the opening 20 minutes. On the quarter-hour James Lambert swung in a corner from the left which was met with a firm header by Gareth Davies. The ball ricocheted goalwards off his team-mate Trevor Morley and was cleared off the line by Vladimir Kinder.
Five minutes later the home side went close again when Martin Williams broke down the right and swept in a cross which Morley directed towards goal, a deceptively lazy swing of his boot producing a stinging shot which Mark Schwarzer in the Boro goal could only parry upwards and inches over the bar.
Boro hit back almost immediately when they struck on the break, Robbie Mustoe feeding Beck who in turn set up Craig Hignett with only the goalkeeper to beat. Nicky Hammond was brave and agile enough, however, to block the shot and put it wide for a corner.
Just before the interval Reading lost their right-winger Williams with what looked like a self-inflicted injury after he had tackled Boro's Andy Townsend, but they came out for the second half with renewed vigour. On 52 minutes Lambert cut in from the left and pushed the ball sideways into the path of the striker Carl Asaba, whose first-time shot produced a fine save from Schwarzer.
On 67 minutes it was the visitors who went closer when Hignett chipped a curling shot from the left corner of the penalty area which struck the angle of crossbar and post.
Then, while extra-time was looming, Townsend's free-kick was headed on by Merson for Hignett to drive in the winner.
Reading: Hammond, Booty, Swales, Lambert, Bernal, Davies, Parkinson, Hodges, Asaba, Morley, Williams (Bowen 44). Subs not used: Thorp, Caskey. Booked: Morley.
Middlesbrough: Schwarzer, Vickers, Kinder, Festa, Pearson, Mustoe, Hignett, Townsend, Beck, Merson, Maddison. Subs not used: Harrison, Moreno, Campbell. Booked: Hignett. Goals: Hignett 89. Att: 13,072.
Referee: G Cain (Bootle).