Gareth Bale's brace earned Tottenham a first league win of the season but only the controversial non-award of a late equaliser denied Stoke a deserved draw.
Jon Walters' 86th-minute header looked to have crossed the line despite Peter Crouch's block, but it was not given.
It meant Bale's double proved decisive, his first bundled home from a yard out and the second a stunning volley.
Ricardo Fuller had poked in to level in between, but in the end Stoke's second-half rally came to nothing.
That was partly down to some wasteful finishing from the hosts - Tuncay in particular the guilty party - while Spurs keeper Heurelho Gomes also produced a couple of excellent stops.
But in the end the game hung on the officials' decision not to award Walters a debut goal following his £2.75m arrival from Ipswich in midweek, a moment that will no doubt heighten calls for video technology to be introduced.
Following summer controversy over Frank Lampard's disallowed effort for England against Germany at the World Cup, this was another example of an occasion when referee Chris Foy could have benefited immeasurably from a video replay.
Tottenham boss Harry Redknapp claimed after the game that a foul in the lead-up to Walters' header should have rendered the debate over whether it had crossed the line redundant anyway.
Either way, though, he will be delighted with a win that sets his side Spurs up perfectly ahead of their crunch Champions League qualifier return leg against Young Boys at White Hart Lane on Wednesday.
It was a victory that did not look in too much doubt at half-time after a first 45 minutes dominated by the visitors.
A spate of injuries meant Redknapp was forced to play Peter Crouch - his only fit striker - up front on his own in a 4-5-1 formation, but Spurs made it work to their advantage with some fine passing and movement across the midfield.
It still took a moment of good fortune for them to take the lead, however.
Aaron Lennon sparked the move with a delightful ball over the top that set Bale in behind the Stoke defence for the first time, and even though his shot was parried by keeper Thomas Sorensen the Welshman was in the right place to deflect home the opener from Ryan Shawcross's attempted clearance.
The hosts responded with typical bite and were level minutes later when Fuller prodded home from close range after Spurs keeper Gomes - claiming a foul by Robert Huth - had got lost under a Matthew Etherington corner.
But Tottenham were in front again minutes later when Bale, picked out by another excellent ball from Lennon, lashed a stunning left-foot volley over the keeper and into the top far corner.
As good as Spurs were in the first half, though, Stoke were better in the second - and only some poor finishing and that late controversy denied them a share of the spoils.
Gomes did well to tip Tuncay's deflected long-ranger over the bar on 70 minutes, moments before the Turkish frontman sent a header wide of the goal unmarked six yards out from a corner.
Shawcross then blazed over from inside the box, Gomes got down well to save from Fuller, and Jermaine Jenas did well to block Matthew Etherington's goalbound shot.
Spurs will take credit for a fine rearguard action in the face of almost constant home pressure towards the end - but in the end Stoke were left fuming with the officials' decision not to award Walters' late strike.
And that misery was compounded after the game with the news that striker Mamady Sidibe could be ruled out for the entire season after snapping an Achilles tendon in the closing stages of the match.
The defeat leaves the Potters pointless from their first two games, though on this evidence they will again cause opposition sides plenty of problems this season.
And as for Tottenham, they will hope their defence - and luck - holds just as well when they host Swiss minnows Young Boys at the Lane on Wednesday.