England boss Gareth Southgate made seven changes to the team which beat Slovenia 1-0 on Thursday.
Harry Maguire and Harry Winks were handed debuts while Jack Butland, Michael Keane and Aaron Cresswell were all given a chance to impress.
And it was Winks who looked the brightest for England in the opening stages.
The away side then went ahead in the 27th minute when Dele Alli was brought down in the box and from the penalty spot, captain Kane stepped up to score off the post.
Marcus Rashford looked lively from his right wing position and after beating two men, his left-foot shot from 12 yards was well saved.
After the half time break, Winks nearly got a goal to cap a fine display but his shot was beaten away by Lithuania goalkeeper Ernestas Setkus.
But the home side were almost allowed a route back into the game when Keane stuck a leg out and deflected the ball towards his own net. Fortunately for the Everton defender, Jack Butland reacted sharply to push the ball way.
Cresswell then had a header tipped away well by Setkus.
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