The Cottagers had lost two in a row in the Premier League (as well as their League Cup defeat to Sheffield Wednesday) but managed to add to their opening day win over Norwich City with another assured home performance.
The Bulgarian produced a customary finish into the top corner which he made look easy when he received a pass from Alex Kacaniklic in the 32nd minute before converting from the spot after Kacaniklic had been brought down in the area on the stroke of half-time.
Seven or so minutes before Berbatov's second, Baggies striker Peter Odemwingie was sent off for a moment of madness when he lashed out at Sascha Riether for no apparent reason with referee Roger East pretty much forced to produce his red card.
Martin Jol's men were again full of attack in the second half, producing a total of 10 shots on goal, but could only add one more as Steve Sidwell wrapped things up in the 89th minute with a volleyed finish from Hugo Rodallega's header back across goal.
It was a disappointing showing from Steve Clarke's Albion side who suffered their first loss of the campaign to fall from third to sixth as Fulham move up to eighth to be the equal top-scoring side in the league with 10 (alongside Swansea and Man Utd).
Craven Cottage, London - 25,691
Yellow cards:FUL - nil WBA - nil Red card:WBA - Peter Odemwingie 38'