The Tottenham striker met James Ward-Prowse’s cross with nine minutes remaining to maintain an unbeaten Euro 2015 qualifying campaign for Gareth Southgate's men
The Tottenham striker found the net with just nine minutes remaining as he met James Ward-Prowse's cross from the right flank.
Gareth Southgate's men had already sealed top spot in Group One before beating Lithuania and have dropped just two points so far in their qualifying campaign.
England struggled to create clear-cut chances in the first half - though Saido Berahino forced a save from Tomas Svedkauskas at close range after 18 minutes - but the best opportunity fell to Ward-Prowse. The Southampton midfielder, however, failed to get his effort on target after being played through by Tom Carroll.
Lithuania went close to taking the lead before half-time as Lukas Baranauskas scuffed effort beat Jack Butland in the England goal but Nathaniel Chalobah was able to clear the ball off the line.
After the break, England looked far brighter and Berahino went close to opening the scoring but was twice denied from inside the box by Svedkauskas.
Nathan Redmond showed quick feet to work a pocket of space inside Lithuania's box but the winger's effort was blocked on the line.
Tom Ince also spurned another opportunity for England as he failed to turn in Luke Garbutt's cross but Kane pounced to seal victory for England, whose final qualification game is against Moldova on September 9.