The midfielder struck at the death as the Bluebirds claimed all three points after Bryan Ruiz had earlier cancelled out Steven Caulker's opener
Steven Caulker put Cardiff ahead with his first goal for the club after 11 minutes, before substitute Bryan Ruiz levelled matters on the stroke of half-time.
Just when it looked as though the sides would have to settle for a point, Jordon Mutch expertly curled an effort past a helpless Robbie Stockdale.
|VIEW FROM CRAVEN COTTAGE
|By Ewan Roberts
The chants of 'JOL OUT!' are growing louder, with Fulham's last win at Craven Cottage coming on April Fool's Day – somewhat apt, many fans will suggest. The Cottagers now have just one point from their last seven home games and remain in the relegation zone after losing against Cardiff City.
The visitors, much to the ire of the home crowd, produced the more inventive football, aided by the confidence of an early lead provided by Steven Caulker's towering header. Martin Jol was forced to make two first-half changes, desperately trying to affect the game, and it was sub Bryan Ruiz who levelled the scores with a crisp, curling effort.
Both sides had chances to take the lead in the second half, but it was not until stoppage-time that one team struck, Jordon Mutch chesting down the ball and rifling the ball into the top corner. The visitors were ecstatic, but time is surely running out for Jol to save his Fulham career.
Peter Odemwingie made his first Premier League start for the club, following his debut appearance in the 1-0 defeat to Tottenham.
Fulham were dealt an early blow when Scott Parker was forced off through injury, with Giorgos Karagounis taking his place.
And Cardiff were ahead after 11 minutes thanks to Caulker.
The club captain and record signing rose above Steven Sidwell to head past Stockdale and edge his side in front.
While the hosts were initially rocked by the goal, Martin Jol's men did enjoy a strong spell of possession during the next 10 minutes but struggled to create any clear-cut chances.
They were almost two down when Ben Turner forced a good save from Stockdale after 26 minutes before hitting the outside of the post with another headed effort just a minute later.
Alexander Kacaniklic was swapped for Ruiz five minutes before the break as Jol looked to invigorate his ineffective forward line.
It paid dividends soon after, with Ruiz levelling for Fulham with his first goal of the season.
The Costa Rican curled home a sumptuous effort from outside the area on the stroke of half-time past David Marshall.
Fulham began the second half well but it was Cardiff who created the first chance, with Fraizer Campbell poking over the bar following a Mutch through-ball.
The home side continued to press but were unable to break down Cardiff's resolute defence before Malky Mackay's men struck in injury time.
Mutch opened his account for the club, curling past Stockdale at the death to extend Fulham's winless run in the league to five.