The tourists had already seized the advantage with a hard-fought 45-run win in the opening match before holding firm in the finale.
Captain Jason Rowles led from the front throughout the two-match series. He amassed 319 runs at an average of 79.75, highlighted by a magnificent 201 in the second Test.
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Josh van Biljon provided excellent support with 233 runs at 58.25, giving South Africa another reliable presence in the middle order.
Bandile Mbatha showed his all-round value, averaging 40.50 with the bat and taking three wickets. Muhammed Bulbulia also contributed 131 runs, while Vihan Pretorius finished with 99.
JJ Basson was the standout bowler of the tour. The seamer claimed 15 wickets at just 12.73, including a superb 7-77 that powered South Africa to victory in the first Test.
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Bayanda Majola added seven wickets as the young Proteas produced a determined team effort away from home.
Some members of the squad will now return to school cricket, while others will prepare for the domestic season. All of them return from England with a series win and another important step taken in their development.
Photo: Proteas Men/X