Australia's loss turned out to be India's gain as Mahendra Singh Dhoni's men rose back to the second spot following the world champions' return to the third position in the ICC one-day rankings issued on Monday.
Australia were unable to complete an unprecedented 7-0 clean sweep over England on Sunday as Ricky Ponting's men went down by four wickets in the final ODI of the series in Durham.
As a result, Australia's brief return to the top of the ODI Championship table ended with the team falling to third again.
South Africa regained the number-one position, the ICC said in a statement.
With just two ratings points separating India, Australia and South Africa, the rankings could be set for some more chopping and changing over the next weeks as the battle for the Champions Trophy begins in South Africa on Tuesday.
England moved back ahead of New Zealand into sixth place in the team rankings.
A reasonable performance in the ICC Champions Trophy could see Andrew Strauss' men make it as high as fourth because they are just four ratings points behind Pakistan in that position.