The spectre of Jose Mourinho hung ominously over Stamford Bridge as the former Chelsea boss, on a spying mission, saw his former charges go behind after four minutes.
Paul Konchesky, wide on the left, sent in a free cross which was missed by centre-back John Terry and Zoltan Gera tucked home from six yards out past a helpless Petr Cech.
Chelsea countered with long-range efforts from Joe Cole and Didier Drogba, but not enough to trouble Mark Schwarzer in the Fulham goal.
Cech was called into action on 33 minutes tipping over a Clint Dempsey half-volley.
Fulham almost stole number two, with 90 seconds of the restart. A poor chest-back by Ricardo Carvalho that was intended for Cech, allowed Bobby Zamora to sneak through and get a left-footed shot in.
Thankfully for Carvalho, Cech was able to smother the chance.
Chelsea responded with a period of sustained pressure on the Fulham defence, which proved a solid resistance for much of the game.
How Chelsea did not score on 56 minutes is a mystery. Salomon Kalou jinked his way to the left byline, sending in a low ball. It passed two Fulham defenders including Schwarzer before the third, Chris Smalling cleared the ball off the line.
A minute later Schwarzer produced a fine diving save to parry away Drogba's left-foot curler.
But on 73 minutes a deep cross by sub Branislav Ivanovic eluded the Fulham back four for the first time and Drogba was on hand to power home a header across Schwarzer and into the far corner from four yards out.
Sixty seconds later and the league leaders went ahead. Kalou sent in a low byline cross and substitute Daniel Sturridge blasted the ball towards goal.
Schwarzer did well to push the ball out but it fell into the path of the luckless Smalling who could only divert the ball into his own goal.
Kalou could have wrapped the game up with seconds to spare but he only rattled the crossbar with a vicious right-foot drive from the edge of the penalty area.
Chelsea now lose Drogba, Kalou and Michael Essien to the African Cup of Nations. But if their nerve and luck hold, they could return to see Chelsea still on top of the league.