Manager Gareth Southgate rates that combination as one of the best in the league and the duo have certainly scored their share of goals this season.
Reading gave a lacklustre performance in the first half and manager Steve Coppell must have given his players a half-time rollocking.
The Royals were more impressive after the break and Middlesbrough were hanging on at the finish following a late goal by substitute John Oster.
Fans will wonder whether this could have been a dress rehearsal for the FA Cup quarter-finals, though both teams face tough replays next week.
South Korea international Lee Dong-Gook was desperately unlucky not to mark his first-team debut with a goal for Boro when he struck a post in the final minute.
He was included in the squad for the first time following an impressive 45-minute appearance for the reserves in midweek.
Reading arrived at the Riverside with an impressive 16 points from a nine-match run.
The visitors were first to threaten when Shane Long outpaced Emanuel Pogatetz but Jonathan Woodgate rescued Boro with a strong tackle.
The home side snatched an early lead with a free-kick straight out of the training ground.
Stewart Downing crossed into the penalty area where Pogatetz headed down for Mark Viduka to backheel the ball into the net from close range. It was the 11th goal of the season by the big Aussie.
Stephen Hunt headed wide for Reading but in general Boro were having the better of the play.
Lee Cattermole struck the top of the crossbar with goalkeeper Marcus Hahnemann back-pedalling.
Yakubu fired a shot into the Reading net, but he was clearly offside and the goal was disallowed.
Royals boss Steve Coppell must have been disappointed with the performance of his side, with Boro goalkeeper Mark Schwarzer untroubled.
Reading opened in a more enterprising mood after the break, but the first danger came at the other end when Viduka fired a 22-yard shot into the arms of Hahnemann.
Leroy Lita made a hash of a scoring chance when unmarked in Middlesbrough's penalty area.
Reading were livelier in this half but it was Middlesbrough who found the target again to double their lead.
From a Viduka pass Yakubu turned quickly and fired a fierce shot into the roof of the net. It was a shot of tremendous power and accuracy for the Nigerian's 16th goal of the season.
Reading substitute Dave Kitson fired a fierce shot over the bar as the visitors tried to pull the game round, before there was a terrific roar from the crowd when Middlesbrough introduced Lee for Yakubu in the closing minutes.
Reading pulled a goal back three minutes from time when substitute Oster scored with a shot from just outside the six-yard box, but Boro held on for the win.