The game was a pretty tame affair up until then, with Arsenal having gone ahead early in the second half thanks to an Aaron Ramsey goal.
Tottenham had been barging down the door until a free-kick was given on the edge of their box.
Christian Eriksen fired in the dead ball as Kane, who was stood in an offside position, was bundled over by Shkodran Mustafi.
The World Cup Golden Boot winner stepped up to bury the penalty and put Spurs level.
The incident will be sure to highlight the need for VAR in the Premier League, as the latest mistake impacts a vital derby.
The Gunners had been managing the game well up until that point, with goalkeeper Bernd Leno having come to the rescure just a couple of times.
Ramsey’s goal originally quietened down a raucous Wembley atmosphere, as Spurs looked to end a run of two consecutive league defeats.
Damaging losses to Burnley and Chelsea respectively have left many speculating that Kane could be looking to engineer a move away from north London if their trophy drought continues.
But if his performance against Arsenal was anything to go by, it still very much looks like he’s got the north London derby fire in his belly.
And with just seconds remaining of normal time, Arsenal received a penalty of their own.
Pierre-Emeriick Aubameyang went down under pressure from Davinson Sanchez – although the decision looked soft.
The Gabon international, however, couldn’t convert the spot-kick, as he watched his effort be saved comfortably by Hugo Lloris.
Th result leaves Arsenal clinging onto a top four place, with Manchester United still to play later.
If United beat opponents Southampton, they’ll catapult themselves into fourth place, with Chelsea still to play on Sunday.
The game ended on a sour note for the Gunners, as Lucas Torreira was sent off for a high challenge on Danny Rose.