A dramatic finish to the game was preceded by a very tight first half with very few chances for either team as both sides battled in midfield.
Manchester City should have opened the scoring in the sixth minute through Paulo Wanchope, but he steered his free header past the post.
As the half progressed Fulham looked to take control through Lee Clark's brawn and Steed Malbranque's brains.
It was Luis Boa Morte who came closest for Fulham in the first half when he flashed his shot across the goal after a twisting run into the box.
The second half exploded into life when Nicolas Anelka scored a lucky opener just after the restart.
Anelka let fly with a 25-yard shot which took a cruel deflection of Zat Knight and past stranded Edwin Van der Sar in the goal.
Manchester City almost went two ahead soon afterwards when Jerome Bonnissel cleared of his own line from a Sylvain Distin shot.
Fulham drew level on the hour when man of the match Malbranque knocked the ball into an empty net after Louis Saha drew David Seaman into a save and squared the ball to his fellow Frenchman.
Fulham, with their tails up, attacked Man City relentlessly and went ahead with just over ten minutes left through the tireless Saha.
Saha chased a long through ball from and beat Seaman to the ball 20 yards from goal. Saha then rounded Seaman and slotted the ball into an open goal from just inside the box.
Man City would not be beaten and this end to end game took yet another turn when Wanchope equalised by heading home his first goal of the season in the dying seconds of the game.
Fulham: Van der Sar, Volz, Goma, Knight, Bonnissel, Malbranque, Legwinski, Inamoto, Boa Morte (Pembridge 84), Clark, Saha. Subs Not Used: Crossley, Melville, Sava, Djetou.
Booked: Clark, Inamoto.
Man City: Seaman, Wright-Phillips (Bosvelt 77), Distin, Sommeil, Jihai, McManaman (Fowler 85), Tiatto, Barton, Sinclair, Wanchope, Anelka (Sibierski 70). Subs Not Used: Weaver, Dunne.
Booked: Wright-Phillips, Sommeil, Anelka, Jihai, Barton. Goals: Anelka 46, Wanchope 90.
Attendance: 16,124
Referee: P Dowd (Staffordshire).