Berbatov laid on Fulham's first, Steve Sidwell's third league goal of the campaign - before coolly side-footing a penalty he helped secure.
The spot-kick finish was just Berbatov's second league goal in 13 appearances this term, and it secured Rene Meulensteen's first win in sole charge.
Should Berbatov sustain the form shown in the first half here, new boss Meulensteen's chances of dragging Fulham clear of relegation danger will increase dramatically.
Berbatov's astute pass sent Alexander Kacinklic haring clear, and he lured Leandro Bacuna into a robust challenge that brought the penalty.
It was a shocking mistake from the Villa full back that condemned Paul Lambert's men to a miserable 2-0 half-time deficit.
The Midlanders were never able to find their stride, eventually suffering their first defeat in six league matches.