It looked like a frustrating night was going to end in defeat when Cameron Jerome bundled in a typically scruffy set-piece goal with just about Stoke's only attack of the second half.
But the lads wouldn't give it up and as we ticked into the third minute of injury time, Gareth Bale whipped in a delightful cross from the left and van der Vaart stooped to glance home from six yards.
Harry Redknapp made four changes to the team that started against Bolton in the FA Cup.
Brad Friedel, Younes Kaboul and Ledley King all returned with Niko Kranjcar starting on the right and Rafa van der Vaart up front with Louis Saha.
The first half was a bright, open affair that we gradually took command of.
Stoke went close through Jerome and Peter Crouch but it was all Spurs from the moment Asmir Begovic made his first save of the night to keep out van der Vaart's 20-yarder.
Bale twice found Luka Modric in the right channel of the box and the Croatian saw both efforts flash across the goal.
Begovic then tipped over Saha's screamer from the edge of the area and we went in at half-time on top.
Jermain Defoe replaced Kranjcar at the break and the second half started in similar fashion as Bale and Younes Kaboul troubled the visitors, but Stoke were clearly now happy to sit back a little further, defend a little deeper and try to hit us on the break.
Giovani entered the fray in the 73rd minute we tried to unluck the door, but the next couple of minutes' action changed the game.
First, Bale's shot clipped off Modric and looked for all its worth that it would loop over Begovic and home, only to come back off the crossbar.
A minute later and having broke up the left side, we conceded a free-kick, Pennant swung it in, Robert Huth's header hit Ryan Shawcross and the ball fell kindly for Jerome to finish from close range.
Van der Vaart forced Begovic into a low save as we pressed forward, the crowd urging the team on as the fourth official showed five minutes of injury time.
Three minutes into injury time, and Bale and van der Vaart delivered - Bale's fine cross from the left found the Dutch striker diving in at the near post to glance home what could yet be a huge goal come May.
Spurs (4-4-2): Friedel; Walker, Kaboul, King (Nelsen, 83), Assou-Ekotto; Kranjcar (Defoe, 46), Modric, Parker, Bale; Van der Vaart, Saha (Giovani, 73). Unused subs: Cudicini, Rose, Livermore, Sandro.
Stoke (4-2-3-1): Begovic; Wilkinson, Shawcross, Huth, Wilson; Diao (Whelan, 27), Palacios (Whitehead, 57); Pennant, Walters, Jerome (Delap, 83); Crouch. Unused subs: Sorensen, Whelan, Jones, Upson, Shotton.
Goals: Spurs - van der Vaart (93); Stoke - Jerome (74).
Referee: Mr M Jones.