In an entertaining game in Kuala Lumpur, Kane broke the deadlock from close range after 19 minutes.
A Danny Rose own goal levelled the scores but Kane restored the Premier League side’s advantage shortly before half-time.
There were no further goals in the second half as both sides made a number of changes but a few of Spurs’ fringe players impressed in the Malaysian capital.
Harry Winks and DeAndre Yedlin were handed starting roles in a??strong line-up while Joshua Onomah, Grant Ward and Kyle Walker-Peters were given opportunities in the second half.
As expected, turnout was low at the??Shah Alam Stadium due to protests from a??Malaysian supporter group that the game was disrupting the??domestic league and Malaysia’s??World Cup qualifying preparations.
But those in attendance enjoyed a bright start from the hosts as they looked lively and caused Spurs problems.
The visitors weathered the storm, though, and took the lead when Tom Carroll’s shot was blocked and PFA Young Player of the Year Kane converted the rebound.
Malaysia then had a goal rightly ruled out for offside but they did equalise in the 32nd minute when a free-kick hit Rose and flew past Hugo Lloris.
The Spurs keeper was called into action to save a shot moving in the air before Kane made it 2-1 late in the half when he finished after a neat one-two between Andros Townsend and Carroll.
The Premier League side made five changes at the break and they dominated the second half without creating too many clear-cut chances.
Erik Lamela dragged a shot across goal,??Onomah fired just wide and Nacer Chadli saw a header well saved as Spurs pushed for a third.
Malaysia also went close with a free-kick but Spurs closed out the game to ensure they head offf to Sydney for the next leg of their tour in a positive mood.