The left-handed batsman slammed two sixes and 10 fours during the course of his first century in South Africa.
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Dhawan reached the landmark during the fourth ODI of the six-match series against South Africa at the Wanderers.
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The 32-year-old, who made his ODI debut in 2010 against Australia, notched up his 13th century off 99 balls to become the ninth batsman overall to etch his name in record books.
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Australian opener David Warner was the last batsman to achieve the landmark, scoring a ton against India in September last year.
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Former captain Sourav Ganguly came close to scoring a century in his 100th ODI before falling for 97 in the 1999 World Cup game against the same opponents.
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Dhawan had scored 35, 51 not out and 76 in the first three ODIs of the series, in which the visitors have already taken an unassailable 3-0 lead.
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Indian opener Shikhar Dhawan, on Saturday, became the first Indian cricketer to score a century in his 100th One-day International.