Switzerland, Denmark, Montenegro, Italy and the Netherlands have also scored more goals than Southgate's England.
Kane dispatched the spot kick with typical confidence, giving the keeper no chance as it crashed in off the post.
The November worldwide break will see them take in home dates against Germany and Brazil, with two of the favourites for global glory expected to help highlight the true state of Southgate's side.
The 21-year-old was one of a number of new faces in the side as Southgate rang the changes with qualification for next summer's World Cup already secured. "I'm proud to wear the shirt and play for England, but these type of games are never easy", he said.
The win saw England finish top of Group F and remain unbeaten throughout the campaign.
Cape Town - England boss Gareth Southgate admits to being impressed with the qualities shown by Harry Kane as captain of the national team. It is now eight internationals since Alli last scored a goal for England, and whilst he is being used in this system, those average displays are only likely to continue.
The downside to the game though was the fact that England struggled to create much more and go on and get more goals in a game that they would have been expecting to do so.
It is now four successive qualifying campaigns that the Three Lions have completed without losing a game.
"Players like Dele Alli and Rashford are exciting but something is missing when they wear the England shirt".
Lallana was named England's Player of the Year for 2016, partly because of his work in between the opposition's midfield and defence.
"They would have to let the ball roll across their body, stop it with their furthest foot, turn in one motion and play the ball forward".
"I think it's important that he is scoring and leading from the front", Southgate told ITV.
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