The defeat means also that Ricky Ponting's Australia will regain their place at the top of the new rankings when the official figures are released later this week.
According to the International Cricket Council (ICC) one-day international predictor, South Africa lost one point after their defeat against Bangladesh and have now moved down to 125, while Australia moved on to 127.
Even a defeat in their latest Super Eights match against England on Sunday would not displace Australia from the top as they will still go to 126.
In case they register a win over their arch rivals they will strengthen their position with one more point (128), the predictor said.
South Africa topped the ICC one-day international rankings at its annual cut-off date on April 1, 2007 for the first time since the rankings were introduced five years ago.
That earned them a handsome cash award of US$175,000, while Australia pocketed US$75,000 for being runner-up.
South Africa's promotion to the top spot was a reward for their good showing in one-day internationals over the past 12 months.
Their performances included a 3-2 series win over Australia on their own soil, during which they clinched the series by chasing a world-record 438-9 last year.
South Africa also reached the semi-finals of the ICC Champions Trophy in India in October 2006, before winning 4-0 against India and 3-1 against Pakistan, both at home.