Heidar Helguson's second-half goal for the Cottagers was not enough to prevent Chris Coleman's side slipping to their ninth defeat on the road.
Alan Pardew unveiled his new £7.5million capture Dean Ashton before kick-off but the former Norwich City striker had signed too late to make his Hammers debut.
So, following their victory at Aston Villa last weekend, West Ham made just one switch as the fit-again Benayoun returned in place of Shaun Newton.
Fulham, who won last time out too, made three changes to the side that beat Newcastle United at Craven Cottage with Carlos Bocanegra, Steed Malbranque and on-loan Wayne Bridge coming into a side still looking for an elusive first away victory of the campaign.
With his World Cup chances diminishing in the wilderness of Chelsea's reserves, Bridge was anxious to impress another man whose England days are now numbered.
And as early as the fourth minute, the watching, under-pressure Sven-Goran Eriksson saw Fulham's borrowed Blue almost mark his debut with a goal when he unleashed an awkward, low 20-yarder that was well held by the relieved Roy Carroll.
And as the West End boys dominated the East Enders in the opening stages, the Hammers keeper was also pleased to see Brian McBride sky over and Helguson's goalbound header blocked by team-mate Luis Boa Morte on the line.
The deadlock just had to be broken. But, surprisingly, it was West Ham who drew first blood when, hampered by Bocanegra, Antti Niemi could only punch Benayoun's 17th-minute corner to the edge of his area where Marlon Harewood nodded on to Ferdinand.
With big brother Rio having scored the winner for Manchester United against Liverpool some 26 hours earlier, Ferdinand the younger refused to be outdone as, back to goal, he swivelled and unleashed an unstoppable, right-footed 18-yard volley that flew beyond the flapping palm of the flying Finn and under his right-hand angle.
Certainly, the ecstatic East Enders reckoned that they had just witnessed Upton Park's goal of the season.
With the half-hour mark approaching, however, Benayoun had other ideas. And when Paul Konchesky and Matthew Etherington combined to square to him on the 18-yard line, Bocanegra proved no obstacle as the Israeli pirouetted one way and then the other before despatching a delightfully delicate 18-yard chip over the Yankee defender, the stranded Niemi and under the bar.
Quite simply, Fulham had been blown away by two moments of Hammers magic and, but for the agility of their keeper, they could have gone off at the interval further behind as Benayoun, Harewood and Bobby Zamora each went close.
With Tomas Repka playing his 188th and final game for West Ham before returning to his native Sparta Prague, the Hammers returned for the restart with their over-enthusiastic PA announcer urging him to bow out with a goal.
But there was still work to be done and, on 53 minutes, the stooping Danny Gabbidon made an embarrassing mess of McBride's flick-on and that enabled Helguson to fire a 15-yarder in-off the stranded Carroll's left-hand post.
The Icelandic international then had a vociferous penalty appeal turned away following Paul Konchesky's challenge and, after McBride also went close, substitute Tomasz Radzinski then forced the Hammers keeper into a spectacular flying save with his first touch.
The arrival of Collins John did not help wobbling West Ham either, and Carroll was soon forced off his line to charge down the Liberian's point-blank shot.
Apart from Zamora's downward header that thumped back off Niemi's left-hand post, West Ham had looked a shadow of the side that had blown Fulham away in the first period but, fortunately for Pardew, the Cottagers could not find the leveller he admitted they deserved and Repka Czeched out of Upton Park a happy man.
West Ham's man of the match: Yossi Benayoun - The immaculate Israeli imp simply ran the show and capped a dazzling display with a magical goal.
Fulham's man of the match: Heidar Helguson - A constant threat throughout, the Icelandic international found the net and with a little more luck might even have earned an equaliser for the Cottagers.