Substitute Jordon Mutch snatched all three points for his side in stoppage time with a curled effort past David Stockdale.
Sports Mole takes a look at where the game was won and lost in London.
On target 5
On target 4
Was the result fair?
Both sides had spells when they were on top at Craven Cottage but Cardiff used the ball better in the final third of the pitch. The visitors created the better chances and therefore deserved to take three points back to Wales.
Martin Jol would have been furious with how his side started the match. The home side looked off the pace for much of the first half, while the partnership between Darren Bent and Dimitar Berbatov just didn't look right. Fulham certainly improved in the second half but they will be disappointed with the number of clear chances they created.
The visitors were excellent this afternoon. Malky Mackay's side pressured the Fulham players all afternoon and the Cardiff manager can be very proud of the way his side attacked their opponents. The equaliser just before half time hurt Cardiff, but they handled the pressure well to claim the victory in dramatic fashion.
Sports Mole's man of the match
Peter Whittingham: There's plenty of contenders for this award, with most of Cardiff's defence delivering a performance good enough to put their names in the hat. However, Whittingham stood out today with his clever passing and direct running at the Fulham defence. The midfielder's deliveries from set pieces cause a lot of problems and he worked hard when his side were under pressure too.
Fraizer Campbell should have secured the victory for his team much earlier in the afternoon. The forward had a great opportunity to score from close range but he somehow managed to scoop his effort over the crossbar. Luckily for Campbell, his error did not come back to haunt him.
Craig Pawson has not been a Premier League referee for too long but he did well on a fairly routine afternoon. Both sides committed plenty of fouls but Pawson kept his cards in his pocket and used good common sense.
Fulham: Jol's men will be looking to recover from this loss and move out of the relegation zone when they host Stoke City next Saturday.
Cardiff: Newcastle United travel to Wales in seven days' time to face a Cardiff team full of confidence following this win.