Arsenal's win at Everton lifted them above their London rivals in the race for Champions League qualification, Spurs' league season continuing to unravel as football returned to White Hart Lane four days after Fabrice Muamba's horrifying collapse.
Cameron Jerome looked to have secured a first ever double for Stoke over Tottenham, but Van der Vaart snatched a point for Harry Redknapp's men, who will need to improve massively to secure a top-four spot that for so long looked theirs for the taking.
No Spurs player took the option of sitting out the game in the wake of Bolton midfielder Muamba's cardiac arrest in Saturday's FA Cup clash between the sides, while both teams warmed up and entered the field of play sporting T-shirts which read "Get well soon Fabrice".
There was also a minute's applause before kick-off, both for Muamba and the medical staff who saved the 23-year-old's life.
Tottenham were guilty of repeatedly giving the ball away early on, with Jerome almost profiting twice.
But it was Van der Vaart who finally mustered the game's first shot on target in the 17th minute of what was his first league start since January.
The first real chances then arrived, near carbon copy efforts missed by Luka Modric in the 18th and 22nd minutes.
Both were supplied by threaded balls from Gareth Bale, but Modric screwed each of his finishes narrowly wide.
The White Hart Lane paramedics, who had been so rapid on Saturday, were poised moments later when Jon Walters was hurt blocking a vicious volley, but the forward was soon back on his feet.
The same could not be said of Salif Diao, who had to be helped from the field in the 27th minute, with Glenn Whelan coming on to replace him.
Spurs were finding it difficult to get in behind their belligerent opponents, despite beginning to dominate.
They almost broke the deadlock from distance six minutes before half-time when Louis Saha's snapshot was tipped over by Asmir Begovic.
With time running out, there were sporadic chants of "Fabrice Muamba", as if the home fans were hoping that might inspire their heroes.
But a yellow card for former Spurs midfielder Wilson Palacios - like Jerome making a rare start for Stoke - was all that really occurred before the interval.
The fouled player, Niko Kranjcar, was replaced at the restart by Jermain Defoe as Tottenham recognised their need for goals.
They were almost gifted one inside three minutes when Stoke's defence presented the ball to Bale but recovered in time to deflect his shot behind.
Defoe then failed to punish an absolute howler from Begovic, the keeper getting his punch all wrong from Ryan Shawcross' miscued clearance and being rescued only by the narrowness of the angle.
Stoke settled and replaced Palacios with Dean Whitehead as Spurs' initial surge subsided into sloppiness.
Tottenham's desperation was all too apparent when Redknapp threw on misfit Giovani Dos Santos for Saha 19 minutes from time and it almost paid off moments later when Bale crashed a dipping 30-yarder against the bar.
But they were instantly behind, their defence failing to deal with a Jermaine Pennant free-kick that Robert Huth flicked on for Jerome to poke home from point-blank range.
Van der Vaart might have equalised but scuffed his finish after collecting Assou-Ekotto's cross and his frustration soon boiled over when he was booked for blasting the ball at the advertising hoardings.
Ledley King was unable to continue after taking a blow to the face and was replaced by Ryan Nelsen, with Rory Delap also coming on for Jerome.
Stoke got yet another block in to thwart Van der Vaart and Bale finally brought the best out of Begovic with a low drive in stoppage-time.
And it was Bale and Van der Vaart who combined as Tottenham snatched would could yet prove a crucial draw, the latter glancing in the Welshman's pinpoint cross.
The game ended in controversy as Pennant stayed down after looking for a penalty, succeeding in running down the clock.