Nolberto Solano's winner, three minutes from time, appeared to roll into the net off the Peru international's arm, but referee Howard Webb rejected the pleas of the home players to the disbelief of manager Roy Hodgson.
The goal, which was as scrappy as the contest that had preceded it, summed up an afternoon which lacked any real spark or quality on an afternoon which was supposed to pay tribute to the only Englishman to have lifted the World Cup.
Bobby Moore may have been remembered in spirit at Craven Cottage but the great man would have been left dismayed by the level of mediocrity on display in West London.
Moore, who represented both clubs with distinction during his career, died 15 years ago on Sunday and, after holding a minute's applause for the defender, many would have hoped that the football on show would pay tribute to such a great player.
Unfortunately, neither team managed to impress, with England head coach Fabio Capello left yawning in the stands.
In a dire first half, neither team managed to produce the type of football that Moore would have admired.
The former West Ham legend would have been perturbed by the way his old club frequently wasted possession, while Fulham, who at times stroked the ball about quite beautifully, looked toothless in attack.
But it was Alan Curbishley's team that should have opened the scoring when Carlton Cole muscled his way through the Fulham defence, only to see his effort brilliantly blocked by Paul Konchesky.
And moments later Cole threatened again, this time sending a swerving volley just inches over Antti Niemi's crossbar with the goalkeeper beaten.
Fulham meanwhile continued to struggle with Jimmy Bullard the only ray of light for Hodgson's side on a grey and gloomy day in West London.
The tousled midfielder was at the heart of everything positive about the relegation-threatened hosts and his pass allowed Paul Stalteri to pick out Clint Dempsey at the near post, only for the American to skew his effort wide of the post.
Fulham improved after the break and almost snatched the lead when Brede Hangeland's powerful header came close to beating Robert Green, only to sail over the crossbar.
With the home side increasing the tempo after a dismal first 45 minutes, West Ham appeared to have lost their way with passes continually going astray.
Mark Noble's flashing effort was a rare glimpse of quality from a team supposedly chasing a place in next season's UEFA Cup, but those aspirations will surely have to be put on hold if this display is anything to go by.
Both Dempsey and Cole wasted half-chances at either end, before Brian McBride saw his close-range effort blocked by Matthew Upson after Paul Konchesky's free-kick had caused panic in the West Ham penalty area.
But despite looking the more likely, Fulham came perilously close to falling behind as Freddie Ljungberg's cross picked out Cole unmarked, only for the striker to somehow head straight at Niemi from six yards out.
But that miss was to prove inconsequential as Solano took advantage of Niemi's poor handling to sweep the ball home with what looked like his arm and hammer another nail into Fulham's coffin.
Fulham's misery was compounded when midfielder Leon Andreasen was sent off deep into stoppage time for dissent.