The division’s leading marksman was perfectly placed to meet Ben Davies’ cross to power a spectacular header past Petr Cech.
Alexandre Lacazette had two glorious chances to rescue something for the visitors, but fluffed his lines on both occasions.
Spurs could have won by more at Wembley had they not squandered countless chances in the second half but Kane’s seventh goal in eight versions of this fixture was enough to seal all three points.
A chaotic opening quarter of an hour had both teams threatening on the counter-attack but it took until the 27th minute for the first real chance to arrive.
Kane should have scored as he drifted beyond Nacho Monreal and Christian Eriksen found him with a clipped cross, but the striker, unmarked, headed over from seven yards.
Spurs settled quicker but in truth the half deteriorated as it went on. Eric Dier could have turned in a skewed Mousa Dembele shot but he also miskicked and by the whistle both teams looked in need of a reset.
When they re-emerged, however, it was Tottenham who grabbed the ascendancy, punching the ball forward faster and harrying their opponents with the sort of aggression Arsenal were either not ready for or simply unable to match.
For the next 30 minutes, Arsenal were hanging on as Kane glanced Dier’s delivery wide and then leathered a volley straight at Cech, after Kieran Trippier had poked the ball through Jack Wilshere’s legs.
Cech, in the spotlight after recent errors, came to the rescue again soon after, with Eriksen’s dipping free-kick heading for the top corner before the keeper tipped it over.
It was just a case of how costly Spurs’ wastefulness would prove as Dele Alli had a glorious chance one against one, but prodded a dribbling finish wide, before Cech denied both Trippier and substitute Erik Lamela from close range.
Lacazette twice should have made them pay for their wastefulness, volleying one chance over and then skewing an even better one wide when Davinson Sanchez got the wrong side.
It tees Spurs up perfectly for their midweek Champions League tie with Juventus and adds further weight to suggestions of a power shift in North London.
Tottenham are now seven points clear of Arsenal in the table, with the Gunners having lost eight games already this season.