Miller reached his hundred off just 35 balls, shattering the record of 45 balls set previously by former Proteas batsman Richard Levi in 2012.
South Africa managed 224 for four off their 20 overs, with Miller not out 101 from 36 balls as he crashed seven fours and nine sixes.
Bangladesh was 141 all out in 18.3 overs, another heavy defeat on a hard five-week tour for the visiting team.More news: Jose Mourinho Reacts Positively To Luke Shaw's Mauricio Pochettino Comments
South Africa whitewashed the Test, ODI and T20I series against Bangladesh.
All through the series, Bangladesh's batsman struggled against the home side's pace bowlers.
South Africa captain Faf du Plessis, who did not play in the T20Is against Bangladesh, said he was proud of Miller's achievement. The first 50 came off 23 balls and the second 50 off just 12 balls as Miller went into overdrive mode. He just missed out on becoming only the third batsman to hit six sixes in an over in worldwide cricket when he could only drive the final ball from Saifuddin through the covers for one. Miller hit six sixes and four boundaries from the 16 balls he faced in this period. Miller joined Evin Lewis and Yuvraj Singh as the only cricketers to hit five or more sixes in an over in a T20l.
Chasing a target of 225, too many of Bangladesh's top order underperformed, with Imrul Kayes, Shakib Al Hasan, Mushfiqur Rahim and Sabbir Rahman all hitting six or fewer. This was a special innings as in getting a century in 35 balls in the course of the 36-ball knock, Miller created an worldwide T20 record.