But his last-gasp effort barely masked a sterile Wembley display by the hosts.
The England skipper pounced from close range to convert Kyle Walker's cross in the 94th minute after a night of frustration for Gareth Southgate's misfiring team in a half-full stadium.
A draw would have sufficed thanks to Slovakia's 1-0 defeat away to Scotland but Kane's effort, his 14th of the season in all competitions for club and country, at least prevented the inevitable boos that would have greeted a goalless stalemate.
It was Kane's second real chance of the evening -- his other effort being well saved by Jan Oblak early in the first half.
England top Group F with 23 points to second-placed Scotland's 17 and have one game to go in Lithuania on Sunday. They have now not lost in 38 qualifying matches.
While England's display will not raise too many hopes of great things in Russia, at least in Kane they have a striker who gives them a puncher's chance of making progress.
He now has 11 goals from 22 appearances for England.
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