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Spurs had trailed to Marc Albrighton’s early goal when van der Vaart headed the home side level in the first half's added time before securing the points with a close range finish 16 minutes from the final whistle.
Van der Vaart's goals came on the back of his effort in the Champions League victory over FC Twente and banished Spurs' fears their domestic form may again suffer in the wake of a midweek European clash.
Villa, who had appeared to be in control of the game before van der Vaart's equaliser, were furious Tottenham’s opening goal was allowed to stand and fell to their first defeat under new manager Gerard Houllier.
The Frenchman's arrival had triggered an upturn in form and there was no doubting the visitors' commitment as they attempted to impose themselves on the game and take advantage of the fact Spurs had come through a testing European tie just four day earlier.
Spurs goalkeeper Heurelho Gomes was twice left needing treatment in the opening 20 minutes after robust challenges, first from Albrighton and then from Stephen Warnock.
Tottenham manager Harry Redknapp was visibly agitated at Villa's approach but he could have no complaints about the build-up to Albrighton's goal that provided the latest example of Emile Heskey's revival under Houllier.
The pair worked together at Liverpool and the former England forward has shown signs of the form he displayed earlier in his career during the three games since Houllier took charge at Villa Park.
This time it was the striker's unwillingness to give up the cause as he chased Sebastien Bassong down that led to a goal.
Heskey harried Bassong into a mistake, snatched possession, and then delivered the ball across the face of the goal after working his way to the byline.
There was still work to do but Albrighton got in front of Alan Hutton to stab the ball home from 2m and give Villa a 16th minute lead.
Spurs struggled to find an effective response until the final ten minutes of the first half when they finally applied more meaningful pressure.
Gareth Bale whipped in a 39th minute cross that Roman Pavlyuchenko should have turned home at the near post instead of simply flashing the ball across Brad Friedel.
But the Russian made up for that miss when he delivered the right wing cross that Peter Crouch sent back across goal where van der Vaart headed in from close range.
The goal came deep into first half added time - too deep for Houllier and the rest of the Villa bench who insisted the half time whistle should have been blown beforehand.
The goal clearly lifted the home side and van der Vaart should have claimed his second six minutes after the break when he shot over from close range.
Crouch followed suit, this time with a header, but the two players then combined much more effectively in the 74th minute to create the winning goal.
Aaron Lennon's cross was headed down by the England striker and van der Vaart claimed his second with a right foot finish from 6m.
