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The 25-year-old has been part of India's T20I squad since July 2023.
India won by 11 runs after posting 219/6 at Centurion.
Suryakumar Yadav-led India had won the first T20I in Durban by 61 runs.
It was Sanju's second T20I ton after the first against Bangladesh in October.
Sikander Raza smashed an unbeaten 133 off just 43 balls.
Sanju Samson smashed his maiden T20I century against Bangladesh to power India to their highest total of 297/6 in the format.
Samson's 111 helped India to their highest T20I score of 297/6.
Sanju's 111 helped India crush Bangladesh by 133 runs in the third T20I in Hyderabad.
Nitish Kumar Reddy hit 74 and bagged two wickets as India won by 86 runs.
The 33-year-old, whose India career came to an abrupt halt after an underwhelming debut in the 2021 T20 World Cup, took three wickets against Bangladesh in the series opener on Sunday night.
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