Dhoni began the series in fifth position in the listings but 177 runs at an average of 59, including 96 in Jamshedpur, has pushed him up the list and he is now just seven rating points behind Australia's Ricky Ponting, who tops the rankings.
India's triumph, which means they have won 17 of their last 22 ODIs, saw them leapfrog New Zealand and Pakistan in the Championship table and they are now just three rating points behind second-placed South Africa.
And if India can win both their upcoming ODIs against Pakistan in Abu Dhabi, on Tuesday and Wednesday, they will reduce that margin to just one point. Australia is 13 points clear of South Africa at the top of the table.
Third place is India's highest position since the Championship table was launched. In April 2005, they were in eighth spot.
Dhoni is one of four India players in the top 20 for batsmen.
Yuvraj Singh is ninth, Dravid is 11th and Sachin Tendulkar, who missed the entire series due to injury, is 18th.
Virender Sehwag, who scored 78 runs in five innings during the ODI series, has dropped seven places in the rankings and is now 28th in the batting list.
All-rounder Irfan Pathan has also made some progress up the Player Rankings.
The left-armer is now fourth in the bowling list, behind South African Shaun Pollock, Australia's Glenn McGrath and Shane Bond of New Zealand and he has eased up to third in the ODI all-rounder's table behind Pollock and England's Andrew Flintoff.
Harbhajan Singh, the leading wicket-taker in the ODI series, is up six places to seventh in the Player Rankings for ODI bowlers while, further down that list, Shanthakumaran Sreesanth, who took 6-55 in Indore, has moved up 32 places to joint 66th with his best-ever haul of rating points.
For England the positives from their crushing series lose come in the shape of James Anderson and Kevin Pietersen, both of whom have made significant strides up the rankings.
Pietersen, the leading run-scorer on either side with 291 runs in five innings, is into the top 10, up eight places to the seventh slot and now has his best-ever haul of rating points. And Anderson, England's most successful bowler in the series with nine wickets, is back into the top 20, up six places to the 18th position.
Pietersen is England's highest-ranked batsman with Flintoff slipping five places to 19th and Marcus Trescothick, who missed the entire Test and ODI series for personal reasons, dropping to joint 20th, alongside Pakistan captain Inzamam-ul Haq.
Stephen Harmison is England's top-ranked ODI bowler in the although he has dropped two places after missing the entire India series through injury, while Flintoff is joint 15th in the list with West Indian Ian Bradshaw.
Further down that list, left-arm slow bowler Ian Blackwell has climbed 36 places to joint 55th, and now sits on the same number of rating points as Kenya's Thomas Odoyo.
England can at least draw a crumb of comfort from their series loss as, although they ended it in seventh place in the Championship table, they were sixth on April 1 and that means they have qualified for the second stage of the ICC Champions Trophy in India.
Pakistan can overtake India and move into third place if they win both ODIs in Abu Dhabi on Tuesday and Wednesday. Two victories would give them 116 rating points and drop India to 114.
LG ICC ODI Championship Table 1. Australia (132), 2. South Africa (119), 3. India (116), 4. Pakistan (114), 5. New Zealand (113), 6. Sri Lanka (105), 7. England (103), 8. West Indies (89), 9. Zimbabwe (42), 10. Bangladesh (24), 11. Kenya (7) LG ICC ODI Player Rankings (Top 10 Batsmen) 1. Ricky Ponting (AUS), 2. Mahendra Dhoni (IND), 3. Adam Gilchrist (AUS), 4. Andrew Symonds (AUS), 5. Graeme Smith (SA), 6. Mike Hussey (AUS), 7. Kevin Pietersen (ENG), 8. Kumar Sangakkara (SL), 9. Yuvraj Singh (IND), 10. Michael Clarke (AUS) LG ICC ODI Player Rankings (Top 10 Bowlers) 1. Shaun Pollock (SA), 2. Glenn McGrath (AUS), 3. Shane Bond (NZ), 4. Irfan Pathan (IND), 5. Daniel Vettori (NZ), 6. Brett Lee (AUS), 7. Harbhajan Singh (IND), 8. Muttiah Muralitharan (SL), 9. Chaminda Vaas (SL), 9. Nathan Bracken (AUS) LG ICC ODI Player Rankings (Top five allrounders) 1. Shaun Pollock (SA), 2. Andrew Flintoff (ENG), 3.
Irfan Pathan (IND), 4. Andrew Symonds (AUS), 5. Shoaib Malik (PAK)