Both sides hit the woodwork while Spurs had another penalty decision in their favour overturned and Bolton were denied a penalty of their own early in the second half.
Spurs pushed for a late winner and their pressure told when Kranjcar, who had only been introduced off the bench with 12 minutes remaining, cracked in a ferocious shot in the second minute of added time.
It did not take long for the game to crackle into life, and Spurs were awarded a penalty after just five minutes of play when the grounded Kevin Davies was penalised for handball as he got in the way of Vedran Corluka's goalbound shot.
Van der Vaart stepped up to stick the ball away with his customary coolness and register his third goal from the spot this season.
Van der Vaart duly obliged, putting the ball in exactly the same place as his first, but he was denied a second goal of the day as referee Mark Clattenburg ordered the kick to be retaken after Wilson Palacios had encroached.
The former Real Madrid ace tried to repeat the feat for the third time in two minutes, but failed, putting his latest effort wide of the mark. It was the fourth time in the last eight attempts that Spurs have missed from the spot this season.
The hosts thought they had yet another penalty just before half-time when Clattenburg again pointed to the spot for another handball. Defoe was quick to grab the ball but he was denied the chance to break his 14-game goal drought when the decision was overruled by the referee's assistant, who had spotted Peter Crouch in an offside position.
The penalty incidents were not the only chances Spurs had to break the deadlock during a frenetic first half; Defoe nodded home on 28 minutes only for his strike to be ruled out for offside and his strike partner Crouch was only denied by a superb last-ditch tackle by Paul Robinson five minutes later.
Bolton could count themselves lucky not to have been down by more than the goal they were at the break, but they too went close to troubling the scorers when Johan Elmander headed off the bar on 21 minutes.
Van der Vaart was withdrawn at half-time and replaced by Steven Pienaar but it was Bolton who made the first telling move of the second half when Sturridge was rewarded for a lively performance with the equaliser 10 minutes after the restart.
The on-loan striker made it two in two games since making his switch from Chelsea, finishing under the body of Heurelho Gomes - who should have done better - after having been played through on goal by Kevin Davies on the counter.
The goal buoyed the visitors and they should perhaps have had a penalty of their own soon after when Gary Cahill appeared to be felled by Pienaar in the box. The whistle sounded, but only to award Spurs a free-kick and for Clattenburg to book the unfortunate Cahill.
Bolton never really recovered from that disappointment and Spurs twice went close to taking the lead again, Jermaine Jenas striking the post with a sublime free-kick and Pienaar only being denied by a point-blank stop from Jaaskenlainen.
But the hosts were not to be denied and Kranjcar's bullet from the edge of the area as time ran out proved decisive and Spurs' campaign to qualify for the Champions League for a second year running remains on track.