The 199-run win, which came with more than a day to spare, was due to Sri Lanka's tireless spin trio of Herath, Akila Dananjaya and Dilruwan Perera who together claimed all 20 South African wickets.
Such was their dominance that home captain Suranga Lakmal, lone paceman in their attack, did not bowl in the first innings and sent down only two overs in the second, preferring to watch his spinners run riot against the leaden-footed South Africans instead.
"There was not much spin as the ball got softer, but we bowled well throughout the series," Herath said afterwards.
Resuming on 139-5 with a comprehensive defeat looming over them, South Africa's end came rather later than expected as the tourists suddenly discovered a stomach for fight which was conspicuously absent in the series.
De Bruyn and Temba Bavuma proved during their 123-run stand that Sri Lanka's rampaging spinners could be tackled with decisive footwork and proper application.
"The guys played well in this last innings," South Africa skipper Faf du Plessis said at the awards ceremony. "Theunis' batting was exceptional and he showed that it's possible to get big runs in these conditions.
"But I have to say 'well played' to Sri Lanka, they were the best team over the last eight days of cricket we played and in all departments," added du Plessis, whose team were beaten inside three days in the series opener in Galle.
De Bruyn registered the first fifty by a South African in the series and soon Bavuma followed suit.
Thanks to their dogged defiance, South Africa had their first century stand in the series and they also breached the elusive 200-run mark.
Both the batsmen generously employed the sweep shot to negate the turning ball but just when it looked like Sri Lanka would endure a rare wicketless session, Herath struck in successive overs to expose the South African tail.
The 40-year-old left-arm spinner drew Bavuma on the front-foot to induce an edge to a sharply turning delivery to Niroshan Dickwella behind the stumps. Bavuma hit four boundaries in his gutsy 63.
In his next over, Herath trapped Quinton de Kock leg before and struck the biggest blow when he uprooted De Bruyn's off-stump after the batsman shoulder-armed to an arm ball.
De Bruyn's stellar 101 - his maiden test century - included 12 boundaries.
Dimuth Karunaratne was the obvious choice for both the man-of-the-match and the man-of-the-series awards for his four 50-plus knocks in as many innings in the low-scoring series.
(Reporting by Amlan Chakraborty in New Delhi; editing by Sudipto Ganguly)
