After the loss in Centurion, South Africa slumped to third position with 123 points while Australia moved up one place to second spot with 125 points. India have 126 points.
India earlier this month had reached the top spot but for barely 24 hours.
With just few points separating the top three teams, more changes are expected as the Champions Trophy progresses.
India, scheduled to play their opening match of the Champions Trophy on September 26 against Pakistan, have 126 ratings points.
South Africa slumped to the third spot after losing last night to Sri Lanka.
South Africa's loss also helped Australia, which gained a place to be second with 125 ratings points.
Sri Lanka occupy the fourth spot, while Pakistan are in the fifth position.
The ICC rankings are set for more changes in the next few days as the Champions Trophy continues.
Published 23 September 2009, 12:45 IST