Dhoni's previous third position was taken by South Africa captain Graeme Smith, who moved up four places following his brilliant run in the current five-match ODI series against Australia at home.
Yuvraj Singh (9th) and Rahul Dravid (10th) retain their places, while Sachin Tendulkar gained two places to move up to 15th, in the Aussie dominated batsmen's list.
Following his 64 against the Proteas in the third ODI yesterday, Ponting swapped places with his vice-captain Adam Gilchrist at the top of the table, with Andrew Symonds (6th), Mike Hussey (7th) and Michael Clarke (8th) following him.
Meanwhile, former South Africa captain Shaun Pollock tops both the bowling and all-rounder lists, riding on his 2-45 and 69 from 74 balls against Australia at Port Elizabeth yesterday.
Pollock was already in top of the bowling chart, maintaining that position ahead of Glenn McGrath, but he now has also overtaken England's Andrew Flintoff in the all-rounder list, which has India's Irfan Pathan in the fourth place just behind Andrew Symonds of Australia.
Australian old warhorse McGrath is in second place in the bowling lists while team-mate Brett Lee is in third and Kiwis Shane Bond and Daniel Vettori are fourth and fifth. respectively .
Three other Proteas are also in the top 20 bowlers list, with Makhaya Ntini, who had a haul of 6-22 in second ODI at Cape Town, is in eighth moving up three places, ahead of Andre Nel (17th) and and Andrew Hall (20th).
In team ratings, Australia continues their reign. But, South Africa can cut the lead to eight points (130 points for Australia and 122 for South Africa) if they can win both remaining matches in the current ODI series. Ponting's side were 19 points clear of the Proteas at the start of the series.
After their 4-1 series win against Pakistan, India are now placed in fourth with 113 points, the same as had by New Zealand, who are in third after calculating to decimal points, following their series victory over West Indies by 4-1 margin.
One-day Team rankings: 1. Australia 132; 2. South Africa 119; 3. New Zealand 113; 4. India 113; 5. Pakistan 112; 6. England 108; 7. Sri Lanka 107; 8. West Indies 89; 9 Zimbabwe 42; 10. Bangladesh 17
One-day Batsmen: 1. Ricky Ponting (Aus) 795; 2. Adam Gilchrist (Aus) 792; 3. Graeme Smith (SA) 757; 4. Kumar Sangakkara (SL) 754,5. Mahendra Dhoni (Ind) 754; 6. Andrew Symonds (Aus) 742; 7. Mike Hussey (Aus) 736; 8. Michael Clarke (Aus) 730; 9. Yuvraj Singh (Ind) 719; 10. Rahul Dravid (Ind) 709; 15. Sachin Tendulkar (Ind) 689
One-day Bowlers: 1. Shaun Pollock (SA) 880; 2. Glenn McGrath (Aus) 775; 3. Brett Lee (Aus) 763; 4. Shane Bond (NZ) 762; 5. Daniel Vettori (NZ) 750; 6. Irfan Pathan (Ind) 737; 7. Muttiah Muralidaran (SL) 710; 8. Makhaya Ntini (SA) 706; 9. Chaminda Vaas (SL) 702; 10. Naved-ul-Hasan (Pak) 678 12. Harbhajan Singh (Ind) 667
One-day All-rounders: 1. Shaun Pollock (SA) 459; 2. Andrew Flintoff (Eng) 452; 3. Andrew Symonds (Aus) 377; 4. Irfan Pathan (Ind) 369; 5. Shoaib Malik (Pak) 358.