The Bulgarian's 52nd-minute strike proved the only goal in what was a fairly turgid encounter at White Hart Lane as the hosts lose their third consecutive match
After a first half with chances few and far between, Berbatov finally opened the scoring just after the interval following a swift counterattack from the away side.
Spurs failed to truly respond to their former striker's goal, with the best opportunities by some distance falling to substitute Jermain Defoe, who could not capitalize on either as Mark Schwarzer produced a couple of excellent saves to deny the Englishman.
As expected, Andre Villas-Boas made several changes from the side that almost capitulated against Inter on Thursday with Hugo Lloris, Caulker, Michael Dawson, Benoit Assou-Ekotto and Gareth Bale coming in for Brad Friedel, Kyle Walker, William Gallas, Jake Livermore and Defoe.
Martin Jol, meanwhile, named an unchanged eleven from the side that earned a hard-fought 2-2 draw away to Sunderland two weeks ago.
Tottenham began the game very much in the ascendancy, with Sascha Riether having to clear an early Bale header off the line after just six minutes, following a dangerous Gylfi Sigurdsson corner.
That was the best chance in what swiftly became a fairly turgid first half as, with both sides struggling to assert themselves on the game, perhaps the most significant incident came from an injury picked up by the talismanic Bale as the Welshman hobbled off gingerly following an ankle complaint just before the interval.
The winger returned after the break but it was Fulham whicj finally sprung the game into life with a goal, courtesy of a swift counterattack finished coolly by Berbatov. Ashkan Dejagah set Riether away down the right, with Spurs short at the back having been caught pushing for the opener, before the right back set the Bulgarian up with a smart cross who duly tucked the finish home to open the scoring.
The visitors were inches away from extending their lead just five minutes later as, after a flick-on from a Giorgios Karagounis corner, Brede Hangeland headed just wide of the far post with Spurs struggling to find a response to Fulham's opener.
With twenty minutes remaining, substitute Defoe finally tested Mark Schwarzer in the Fulham goal, though the Australian proved more than equal to his stinging effort from the edge of the box, palming away adeptly.
Schwarzer was to thwart Defoe once more in the last chance of the game, producing an absolutely magnificent save to deny the Spurs frontman after Bale put the ball on a plate for Defoe in the six-yard box and, in doing so, retaining his clean sheet and securing a win for the away side.