Vaughan senior, who has been in Australia this summer working as a commentator on the India series, led his country in 51 Tests, but beforehand skippered his country at under-19 level in 1993/94.
Son Archie, who broke into the Somerset side as spin-bowling all-rounder last season, has now been handed the same honour for the forthcoming tour of South Africa.
His side will take on the Proteas in three Youth ODIs and two Youth Tests in Cape Town and Stellenbosch between January 17 and February 6.
"To get the opportunity to represent England at this level is really special in itself, but to lead the team out is something else," said the 19-year-old.
"If someone had told me 12 months ago that I would have forced my way into the Somerset first team and be captaining the under-19s, I wouldn't have believed them.
"It's happened quickly but I'm going to keep my feet on the ground and work harder and harder.
"The next step is to try and win in South Africa and hopefully I can perform as well."
The 18-man squad is overseen by head coach Michael Yardy and includes 16-year-old off-spinner Farhan Ahmed, younger brother of England international Rehan, highly-rated leg-spinner Tazeem Ali and Durham's pace prospect James Minto.
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