Fulham had originally led through Diomansy Kamara, before Roman Pavlyuchenko equalised just a minute later in the first half.
Huddlestone’s second half strike had originally been ruled out by referee Mike Dean, who overturned his decision to anger the hosts, who ended an unbeaten run against Spurs in the Premier League that stretched back to March 2002.
Spurs started the brightest and had two chances through Pavlyuchenko inside the first five minutes, first meeting a cross with a header that was deflected clear by Hangeland, before failing to squeeze a shot into Schwarzer’s far corner.
Brazilian Sandro, making a surprise start at Craven Cottage, then went close on the 10 minute mark, but his shot from distance sailed wide.
But Fulham were soon in the ascendancy and the best chance of the opening exchanges fell to Diomansy Kamara, who rose to meet a Davies corner, only to glance his header narrowly wide.
Similarly, Hangeland was presented with a headed opportunity minutes later as Modric gifted the ball to Davies in the Spurs area, but the Norwegian nodded over.
Fulham largely handled Spurs' attacking threat of the likes of Gareth Bale early on and Clint Dempsey was the next player to go close, curling in a long range shot that again, narrowly missed the target.
And the hosts took the lead on the half hour mark, as Mousa Dembele chested down a long ball, turned and crossed for Kamara, who tapped home.
Spurs responded no more than a minute later though as Van der Vaart swivelled on the ball in the Fulham penalty area and watched his lob clear Schwarzer and hit the crossbar, before Pavlyuchenko stroked the ball into an empty net.
With three minutes before the interval, Dembele and Kamara again combined, as the latter forced a magnificent diving save from Heurelho Gomes at full stretch.
Kamara’s effort was the last action of the half, though Ledley King was forced to trudge off disappointingly with a knock to his troublesome knee to be replaced by Sebastien Bassong, leaving him a doubt for Wednesday’s Champions League tie.
The visitors started the second half without Sandro, who was replaced by Aaron Lennon, which allowed Van der Vaart to move into a role just behind Pavlyuchenko.
Indeed the Dutchman was nearly the hero shortly after as he met a low cross, but was denied from close range by the frame of Schwarzer.
Fulham were then forced into a change as captain Danny Murphy was replaced by Stephen Kelly.
But it was Redknapp’s tactical change that appeared to pay dividends as Spurs looked an improved side in the second half.
As the visitors continued to press, the moment of controversy arrived. Huddlestone blasted an effort from 25 yards into Schwarzer’s bottom right hand corner, before referee Mike Dean ruled the strike out for offside. After consulting one of his assistants though, Dean overturned the decision and awarded Spurs the goal, much to the home side’s fury.
Kamara then had the chance to level as a high ball fell into his path, but he seemed surprised by the chance and half-heartedly stuck a foot out which left Gomes with a comfortable save to make.
Huddlestone went close with another drive from distance but could only smash the ball into the crowd behind the goal, before Peter Crouch replaced Roman Pavlyuchenko.
Mark Hughes made changes in an attempt to save the game, but Fulham were unable to breach the Spurs defence, who held on to secure a vital London derby win.
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