Viduka and Hasselbaink combined well
Mark Viduka scored on his debut for Middlesbrough as Steve McClaren's side moved out of the bottom three with their first win of the season.
The Australian was able to play for the first time after completing a two-game ban incurred while a Leeds player.
He scored in the 54th minute, driving home after being set up by strike partner Jimmy Floyd Hasselbaink.
Fulham were put to the sword 12 minutes from time as Szilard Nemeth rifled home from a cross by Franck Queudrue.
Viduka wasted the best chance of the first half, shooting straight at Edwin van der Sar after he was put through by Bolo Zenden.
Fulham's summer signing Tomasz Radzinski looked the most threatening, troubling Middlesbrough on more than one occasion.
The most dangerous chance created by the Canadian saw Mark Schwarzer clear with Andy Cole about to pounce.
In the second half, though, Middlesbrough began to take control with Viduka and Hasselbaink linking up well.
It was Viduka who broke the deadlock in the 54th minute, as Hasselbaink took a pass from Gaizka Mendieta and found the Australian, who steered home.
Hasselbaink soon went close himself before Boro made it 2-0 in the 78th minute - Nemeth receiving Queudrue's pass on the right-hand side of the box and driving home.
Fulham: Van der Sar, Volz, Bocanegra, Goma, Knight, Legwinski,
Diop (Boa Morte 74), Radzinski, Jensen, John (McBride 62), Cole.
Subs Not Used: Crossley, Pembridge, Bonnissel.
Middlesbrough: Schwarzer, Queudrue, Riggott, Southgate,
Parnaby, Boateng (Doriva 89), Mendieta (Nemeth 77), Parlour,
Zenden, Viduka (Job 71), Hasselbaink.
Subs Not Used: Nash, Cooper.
Goals: Viduka 54, Nemeth 79.
Ref: D Gallagher (Oxfordshire).