Set 192 to win in Hampshire, the hosts were dismissed for 101 and it meant they suffered their joint-biggest defeat in this format and went a first home summer since 2013 without winning a limited overs series.
It continues the tough start to life as England's white-ball captain for Buttler, who replaced Eoin Morgan in June and saw trusted ally Ben Stokes retire in shock circumstances from 50-over cricket a month later.
India had already won two limited-overs series against the hosts by that point and this loss to South Africa, who were indebted to half-centuries by Reeza Hendricks and Aiden Markram in a total of 191 for five, leaves the home side low on confidence before this winter's T20 World Cup.
Buttler and new head coach Matthew Mott do at least have seven T20s pencilled in for September away to Pakistan and the duo will hope confidence can be repaired there before attention fully turns to Australia where England may suddenly not be among the favourites to lift silverware.
Defeat in Cardiff on Thursday had set up a winner takes all clash at the Ageas Bowl where the new captain again won the toss and fielded first, which looked a wise decision when the recalled David Willey sent Quinton De Kock back for a three-ball duck
Rilee Rossouw responded with an entertaining knock of 31, which included four boundaries off a single Chris Jordan over, but was accounted for by Moeen Ali after the first of two mini rain delays in Hampshire.
South Africa went six overs without a boundary during the middle part of their innings, but Hendricks remained busy with a succession of singles and twos and found able support in Markram, who was back in the T20 side for the first time since last year's World Cup.
Hendricks did eventually move through the gears before his third fifty of the series ended on 70 while visiting captain David Miller blitzed 22 off nine balls only to see his fun come to an end via the excellent Willey, who claimed two scalps at the death.
It was the expensive nature of Reece Topley and Jordan which initially cost England with the seamers going for a combined 97 runs to help South Africa set 192 for victory, which proved far too many for the hosts' underperforming batting line-up.
The hosts required a big contribution from the out-of-sorts Jason Roy but he saw opening partner Buttler go first when the skipper edged Keshav Maharaj to Lungi Ngidi at short third man to depart following another low score.
Roy trudged off soon after after making only 17 to already leave England up against it and South Africa were not able to let their stranglehold on the clash go to waste.
Dawid Malan and Ali went for single-figure scores, the latter to a sensational one-handed catch from Tristan Stubbs, with Jonny Bairstow fighting a losing battle down the other end.
Tabraiz Shamsi got in on the act when he tempted Liam Livingstone into a false shot and would eventually claim a five-wicket haul as England's chase never truly reached second gear.
Shamsi's ended with five for 24 but it was fellow spinner Maharaj who had the last word when Bairstow's lone vigil of 27 from 30 balls came to its conclusion with a slog-swept caught by South Africa captain Miller.
It saw England dismissed with 20 balls to spare to leave Buttler and Mott with problems to solve before another vital trip Down Under this winter.