The Bulgarian forward was in fine form as he netted a wonderful strike from inside the box before converting a penalty, with Steve Sidwell adding a late third for the hosts
The Bulgarian striker netted twice in the first half, the first a wonderful effort into the top corner before a second was added on the stroke of half-time, with Baggies attacker Peter Odemwingie seeing red for a senseless kick out five minutes previously.
Sidwell wrapped up a deserved victory moments from the end, crashing a half-volley into an unguarded net after a mix-up in the area.
Martin Jol named an attacking line-up, with Berbatov making his home debut for the club, but looked a little short in the centre of midfield as Chris Baird deputised alongside Sidwell.
Steve Clarke only had one change to make to the side who beat Everton 2-0, with Billy Jones coming into the team for Steven Reid at right-back.
Fulham started brightly, and almost took the lead when Berbatov tried to get on the end of Sascha Riether's cross, but Jonas Olsson was there to prevent the striker getting a telling touch.
The first real effort of the game came when James Morrison fired in an effort from the edge of the area, with Mark Schwarzer tipping over well. Billy Jones then put in a dangerous ball across the six-yard box, but no-one was on hand for a tap in.
Fulham were pressing more and more as the first half wore on, and eventually found an opener just after the half-hour mark. Alex Kacaniklic had been finding space time and time again to run at Jones, and on this occasion he found Berbatov, who had time to take a touch and curl home a great effort into the top corner around approaching defenders and Ben Foster in goal.
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And as the first half entered stoppage time, it looked to be all over as Kacaniklic rampaged down the left again, being brought down by Jones in the area for a clear penalty. Berbatov stepped up and made it look simple, sending Ben Foster the wrong way to double the lead at half-time.
The second half started with a double swap for the visitors as Marc-Antoine Fortune and Shane Long were replaced by Romelu Lukaku and Chris Brunt, and for a while the game lacked any real sort of tempo.
However, as the half progressed, Fulham’s dominance again grew, with attack after attack being launched on the Baggies' goal, and only Ben Foster really impressing for the visitors.
Sidwell then wrapped up the game as he crashed in a rebound after Rodallega's header hit the bar following good work from substitue Pajtim Kasami.