Earlier, the world record of the fastest T20 global century was named by South African batsman Richard Levi against Kiwi team in Hamilton in 2011/12.
Miller produced a scintillating knock as he hit an unbeaten 101 off 36 balls (seven fours, nine sixes) and handed the Proteas a 2-0 series victory and with it, a historic clean sweep across all three formats against Bangladesh.
Bangladesh was 141 all out in 18.3 overs, another heavy defeat on a hard five-week tour for the visiting team.
While South Africa gained valuable preparation under new coach Ottis Gibson ahead of tours by India and Australia, Bangladesh failed to live up to the promise it showed recently in home series.
Shakib Al Hasan led Bangladesh in the two T20Is against South Africa. Miller hit six sixes and four boundaries from the 16 balls he faced in this period.
Bangladesh came closest to something to celebrate when it went down by 20 runs in the first T20.
Cricketers to score a T20I century at a position lower than No. 4 - Miller is the first one to do so.
David Miller scored the fastest hundred in global T20 cricket off 35 deliveries - including five maximums in a row in the 19th over - to finish 101 not against Bangladesh.
The 28 year-old Miller said after the game: "It is pretty special".
To make matters worse for Bangladesh, Miller was dropped second ball as a diving Mushfiqur Rahim just failed to hold from a gloved Rubel Hossain bouncer down the leg side.
Before Miller arrived South Africa was only 78-3.