The tottenham striker had previously given England the lead, but after they were pegged back by Ferjani Sassi's penalty it looked as though they were going to be left frustrated.
For all their huff and puff, England were unable to blow the Tunisians' house down, with Nabil Malloul's side being relatively untroubled in the second half despite long spells of England possession.
However, with 91 minutes on the clock the pressure told. Kieran Trippier swung in a corner from the right and Harry Maguire nodded it into the path of Kane at the far post, with the England skipper arching his neck muscles to power home to give his side victory.
The win moves England joint on points with Belgium at the top of Group G, with the 'Three Lions' next in action against World Cup newcomers Panama on Sunday.