The Bulgarian opened the scoring for the Cottagers before a Hugo Rodallega header and late Joey O'Brien own goal wrapped up the points for Martin Jol's men.
The Bulgarian was on hand to give his side an early lead, when he headed home Damien Duff’s free kick.
Kevin Nolan leveled things for the Hammers after the break, but Fulham soon regained the lead through Hugo Rodallega, before a Joey O’Brien own goal wrapped up things for the Cottagers late on.
After an even start to the game, in which few chances were created, Fulham slowly started to assert themselves in front of their home crowd, and could have taken an early lead through Bryan Ruiz, only for his powerful effort to be well-saved by Jussi Jaaskelainen.
The Cottagers did not have to wait long to take the lead however, when Duff’s crafty free-kick evaded everyone in the centre, allowing the talismanic Berbatov to sneak in at the far post and beat Jaaskelainen at his near post with a downward header.
West Ham fought back as the half wore on, but struggled to create anything in attack, with Matt Jarvis heading a rare Hammers chance over the bar when well-placed at the far post.
With both sides defending valiantly, Berbatov almost doubled his side’s lead with a moment of brilliance just before the interval.
The Bulgarian shrugged off two West Ham players on the halfway line before going on a mazy solo run, but Jaaskelainen was more than a match to the Bulgarian’s low, driven effort from the edge of the area.
West Ham upped the tempo after the break as it peppered the Fulham penalty area with balls into the box, and it was soon back on level terms.
Shaping up to cross a free kick into the box, Mark Noble played a quick through ball forward to Nolan, allowing the West Ham captain to unleash a thunderous first time effort at goal, which sailed through Mark Schwarzer’s legs into the bottom corner.
The Hammers were back on level terms for just a minute however, as Rodallega soon restored the Cottagers’ lead.
Duff turned provider once again, as his cross from the left found the Columbian, who out-jumped three West Ham defenders to head home from close range.
Despite restoring its lead, Fulham continued to look rattled in attack, as West Ham pressed forward searching for another equalizer.
Each side continued to exchange attacks, with Nolan going close for the Hammers, before Berbatov was once again came close at the other end, his rasping effort from just inside the penalty area, drifting cruelly wide of Jaaskelainen’s far post.
West Ham brought on Carlton Cole and Andy Carroll as their quest for an equalizer continued, with the latter almost making an instant impact, volleying an effort at goal which Schwarzer did well to keep out.
Substitute Mladen Petric made sure of the result late on, as O’Brien deflected his chipped effort past the stranded Jaaskelainen, as Martin Jol’s side secured only their second league win from their last eight games.
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