Goals from Darren Ambrose, Patrick Kluivert and Shola Ameobi were enough to sink the Cottagers.
Newcastle headed to London hoping to end a disappointing season on a high, but there was no place in the side for Alan Shearer who did not even figure on the bench for Graeme Souness' team.
After a slow start to the game it was former Ipswich Town star Ambrose who made the first impact with an 18th minute opener.
Charles N'Zogbia crossed from the left and, after James Milner's header had bounced back off Fulham defender Liam Rosenior, Ambrose pounced to smash the ball beneath Edwin van der Sar.
Fulham provided little threat in the opening period and it was Newcastle who had the next sight on goal after 28 minutes.
Milner's cross found the head of the unmarked Kluivert, but the Dutchman was unable to hit the target with his effort.
Soon after Fulham finally had a glimpse of a chance but Lee Clark headed just over.
The slow pace continued after half time but it was Newcastle that always looked likely to score, and eventually they doubled their tally.
Kluivert raced in at the near post after 61 minutes to meet N'Zogbia's corner and leave van der Sar with no chance.
But the Cottagers' fate was sealed on 74 minutes when Ameobi rose high above the Fulham defence to power a far post header beyond the Fulham keeper from a Milner corner.
Tomasz Radzinski scored a late consolation for Chris Coleman's side when he latched on to Rosenior's throughball before firing past Shay Given - but it was far too little too late for Fulham.