The former Manchester United striker produced a moment of brilliance to secure all three points for the hosts and move them up one place into 11th in the Premier League table
The Bulgarian rifled home in first-half stoppage time after the Potters failed to clear Sascha Riether's searching cross from the right to take his tally to nine goals for the season.
Martin Jol made three changes to the side that drew 0-0 with Norwich last time out, with Ashkan Dejagah, Giorgos Karagounis and Riether all starting, while Geoff Cameron and Marc Wilson came in for Stoke.
A lively start to the match saw presentable chances squandered by both sides as first Jonathan Walters wasted an opportunity to really test Mark Schwarzer before Berbatov volleyed over the top after good work on the right flank by Riether.
The hosts did have the ball in the net in the 11th minute although referee Lee Probert correctly ruled that Bryan Ruiz had used his hand to convert following Damien Duff's delicious in-swinging free kick from deep.
Steven N'Zonzi, who was visibly riled after taking a whack in the face from a flailing Berbatov arm just minutes earlier, was then perhaps fortunate to escape with only a yellow card after pushing Ruiz in the face.
And Karagounis nearly made the Potters pay from the resulting free kick, with his curling effort forcing Asmir Begovic to palm over the top of his crossbar.
Jol's men would go into the half-time break with a 1-0 lead, however, with Berbatov the man of the moment as, in first-half stoppage time, he arrowed a sublime volley into the top corner after Robert Huth had only half-cleared Riether's cross.
A defensive error nearly cost the hosts almost immediately after the restart as Philippe Senderos attempted to block off Peter Crouch only for the former Tottenham striker to nip in front of his man, forcing Schwarzer to rush out and smother.
Schwarzer was again called into action as this time he denied Stoke from the penalty spot. Dejagah was penalised for handball in the box and Walters stepped up only to see his spot-kick saved low to the Australian's right.
Fulham almost doubled their advantage shortly after as Berbatov produced a couple of nonchalant flicks to get away from Huth but his awkward low volley was gathered at the second attempt by Begovic.
Brek Shea, who had replaced Matthew Etherington in the first half, then struck a fizzing low shot just wide before John Arne Riise had Begovic worried in the 64th minute with a bending effort that drifted just over the top.
Fulham looked the most likely to score the game's second goal as we entered the latter stages with Karagounis blasting over the top after cutting inside from the left flank before Ruiz jinked past Ryan Shawcross and into the box but he ultimately failed to deliver the telling final pass.
Even with the introductions of Cameron Jerome and Kenwyne Jones, Stoke failed to find an equaliser, with the result moving the hosts up to 11th in the table, one point behind Tony Pulis' men in 10th.