The 31-year-old, making his first start since a deadline-day move from Manchester United, opened the scoring in the 32nd minute of Saturday's clash at Craven Cottage before adding a second from the penalty spot on the stroke of half-time, with Steve Sidwell adding a third in the closing stages.
West Brom forward Peter Odemwingie was sent off in between Berbatov's strikes for violent conduct as Steve Clarke's side lost their first Premier League game of the season.
The second-half was noticeable for a string of superb saves from West Brom goalkeeper Ben Foster as Fulham failed to add to their lead until the last minute when Sidwell volleyed home.
The home side dominated possession in the opening stages as they pinned West Brom onto the edge of their own penalty area but it was Baggies' winger James Morrison who produced the first effort of quality.
On a rare early foray forward the winger, who signed a new contract yesterday, collected the ball from Billy Jones before forcing a smart save from Fulham goalkeeper Mark Schwarzer.
Jones then pulled a low cross back across goal but neither Shane Long or Marc-Antoine Fortune had gambled on making a run and the ball was eventually cleared.
Fulham's early dominance subsided but they were still looking lively in the final third without testing Foster in the visitor's goal and the final ball lacked quality on a number of occasions.
Berbatov's goal came just after the half-hour mark following some good work from Alex Kacaniklic.
The young winger showed good feet when surrounded by three West Brom defenders before rolling the ball into Berbatov who bent his effort inside Foster's left-hand post.
West Brom came close to an immediate equaliser as Berbatov fouled James Morrison and from the resulting free-kick Fulham skipper Brede Hangeland managed to throw himself in from of Jonas Olsson's shot to keep his side ahead.
Moments later West Brom were reduced to 10 men when Peter Odemwingie was shown a straight red card by Roger East for kicking out at Sascha Riether right in front of the dugouts.
Berbatov, who seemed to be at the centre of all of Fulham's decent play, came close to adding a second in the 40th minute but his diving header flew past the post.
The hosts were awarded a penalty in first-half injury time when Jones fouled the busy Kacaniklic after the 21-year-old had beaten him for pace inside the box.
Berbatov stepped up confidently and sent former Manchester United team-mate Foster the wrong way to double Fulham's lead at the interval.
Clarke made two changes at the start of the second-half, replacing Long and Fortune with Chris Brunt and Romelu Lukaku.
But it was Fulham who continued to press, looking to make their numerical advantage count.
Brunt forced Schwarzer to tip a long-range effort over the crossbar just after the hour and the Northern Ireland midfielder's corner then hit the outside of Schwarzer's post.
Clarke's other half-time introduction then tested Schwarzer as Lukaku was picked out by Brunt before shooting low and hard at the Australian.
Foster then made a low save from Sidwell's long-range effort and managed to claw the loose ball away from the on-rushing Damien Duff.
The former England goalkeeper then palmed Duff's own deflected shot from the edge of the box behind for a corner as Fulham started to take a stranglehold on proceedings.
Only Foster was keeping West Brom in the game as he once again did superbly well to tip Hugo Rodallega's shot around the post after more probing play from Duff.
Despite struggling to maintain Fulham's attacking players, Clarke decided to introduce Markus Rosenberg from the bench with 15 minutes remaining in an attempt to claw a goal back.
Foster continued to pull off save after save and denied both Berbatov and Rodallega towards the end of the game.
But he was powerless to stop Sidwell adding the third with only a minute to go.
Foster kept substitute Pajtim Kasami's front-post cross from sneaking in before Rodallega headed the rebound onto the crossbar.
The loose ball fell to Sidwell who lashed the ball into the empty net.