Darren Bent climbed off the bench to fire Fulham to their first home win in almost six months.
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Everton looked set to ease in to the fourth round of the Capital One Cup after dominating the first half and they took a well-deserved lead through Steven Naismith.
Romelu Lukaku and the excellent Gerard Deulofeu kept Everton on top, but they could not find a second and Fulham made them pay as Martin Jol's men ran out 2-1 winners.
Jol's side had lost five and drawn one of their previous six home games, but Dimitar Berbatov levelled with his first of the season and Bent then wrapped the win up in front of England manager Roy Hodgson less than three minutes after his introduction from the bench.
The Fulham fans who chanted "Jol out" 10 days ago cheered the Dutchman and his men off after a welcome win for the west London club.
Roberto Martinez, on the other hand, will travel back up to Merseyside not knowing how his team failed to win after dominating the first half.