Australia, who reigned at the top since the introduction of the championship in 2002 till last month, tied on equal points (127) with the Proteas but lost out after calculation on decimal points as the cut-off date for the announcement of annual championship table ended yesterday.
The Aussies will have to satisfy with runners-up prize money of 75,000 dollar, though they could take solace in the fact that they remained ICC Test Champions for the third year in a row and will receive a further 175,000 dollar for that achievement.
Graeme Smith's side dethroned Australia from the top slot of the ODI chart last month following an outstanding run of success over the past year which saw the them win 15 of their 21 ODIs ahead of the ongoing World Cup and three out of four matches since the showpiece event began.
Although South Africa lost to Ricky Ponting's men in their Group A game in St Kitts last week, it was not quite enough for the Aussies to dislodge the Proteas from top spot.
In the end, South Africa's one-wicket victory over Sri Lanka in the Super Eight stage in Guyana on Wednesday proved to be the result that took them over the top, giving them a wafer-thin lead of just 0.1199 ratings points.
''I'm delighted that we are top of the ODI Championship and I think it is a just reward for all the hard work and dedication the guys have shown over the past 18 months or so,'' said Smith.
''That said, although this is very pleasing for us it will not detract us from the immediate job at hand. We are completely focused on the World Cup and we want to do the very best that we can while we are here in the Caribbean,'' he said.
The Proteas have had an extraordinary run of form over the past 12 months. This includes a 3-2 series win over Australia, sealed by scoring a then world-record 438-9. Since then South Africa has continued their good form, getting to the semi-final of the ICC Champions Trophy in India.
But with the table so tight at the top, Ponting's team can get back on top if they continue to perform as they have done so far in the World Cup.
If both Australia and South Africa win their remaining Super Eight games then the Proteas will progress to the semi-finals as the world number-one ranked ODI team.
But if they falter along the way, even once, and Australia remain unbeaten, then Ponting's men will make a rapid return to top spot by the time the tournament is reduced down to last four.
Meanwhile, further down the Championship table, there is still plenty of movement possible over the coming weeks. Just 13 rating points separate New Zealand in third (115) and West Indies in eighth (102).
With fourth-placed team Pakistan and sixth-placed India having been eliminated in the group stage, there is an opportunity for the likes of the West Indies, England and Sri Lanka to move up the rankings if they can discover that winning feeling in the remainder of the Super Eight.
It is the third year in a row that Australia has won the ICC Test Championship and in the past 12 months it has played seven Test matches and won all of them. That included all five Tests against England as Ponting's men become the first Australia team to win all matches in an Ashes series since the Warwick Armstrong-led side of 1920-21.
LG ICC ODI Championship Table: 1. South Africa (127); 2. Australia (127); 3. New Zealand (115); 4. Pakistan (110); 5. Sri Lanka (108); 6. India (106); 7. England (105); 8. West Indies (102); 9. Bangladesh (44); 10. Zimbabwe (22); 11. Kenya (0) LG ICC Test Championship Table: 1. Australia (135); 2. England (114); 3. Pakistan (108); 4. India (107); 5. Sri Lanka (102); 6. South Africa (102); 7. New Zealand (93); 8. West Indies (72); 9. Zimbabwe (28); 10. Bangladesh (2)