The last time South Africa headed the ODI rankings was in September 2009 but they slipped down the standings after their first round elimination from the ICC Champions Trophy at home later that month.
South Africa trailed Australia by one point before the three-match ODI series against New Zealand and though the third and final match in Hamilton was washed out on Monday, the 2-0 result was enough to take them up to the top of the table.
The number one ranking comes as a welcome boost for the side ahead of the 50-over World Cup being held in Australia and New Zealand early next year.
Reigning world champions India are in third spot while 2011 runner-up Sri Lanka are next with four points separating the top four nations.
South Africa captain AB de Villiers also retained top spot in the batting rankings with team mate Hashim Amla overtaking India's Virat Kohli to claim second.
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