Viduka netted Boro's first after 54 minutes, with Szilard Nemeth securing the points with a second 11 minutes from time.
It is Viduka who will dominate the headlines though, linking up well with new strike partner Jimmy Floyd Hasselbaink and posing a constant threat to the Fulham defence.
The bulk of the attacking play came form the visitors, but in between times Fulham's midfield duo Papa Bouba Diop and Sylvain Legwinski ran the game.
However, the Cottagers lacked invention and rarely posed a threat up front after the opening stages, when Tomasz Radzinski headed a Claus Jensen free-kick over the crossbar.
Bolo Zenden caused havoc on the left during the first half but was unable to produce a telling final ball and Boro had to rely on long-range efforts from Ray Parlour and Hasselbaink.
Visiting keeper Mark Schwarzer was called into action to keep out a Collins John header midway through the first half, but Boro had the best of the chances before the break – Viduka seeing an effort parried by Edwin van der Sar and Stuart Parnaby pulling a shot wide.
Straight after the interval Hasselbaink played in Viduka, but the Australian's control let him down - minutes later he made no mistake.
Gaizka Mendieta fed Hasselbaink, who supplied Viduka and the former Celtic man steered the ball home to break the deadlock.
Viduka was replaced in the 71st minute and Boro almost paid the price immediately when Radzinski was inches away from getting on the end of Carlos Bocanegra's cross.
However, the result was put beyond any doubt when Zenden combined with Franck Queudrue to supply substitute Nemeth, who bundled the ball home at the far post.