During the series between India and Australia in 2009, Dhoni hit an aggressive 124 runs in just 107 balls, in the second ODI, and a measured knock of 71 runs in 95 balls, along with Yuvraj Singh and saw India home by 6 wickets in the third ODI. Dhoni took his first and only wicket in international cricket on 30 September 2009. He bowled Travis Dowlin of the West Indies during a match in the 2009 ICC Champions Trophy.
Dhoni topped the ICC ODI Batsman rankings for several months in 2009. Michael Hussey from Australia replaced him at the top spot at the beginning of 2010.
Dhoni had an excellent year in ODIs in 2009, scoring 1198 runs in just 24 innings, at an astonishing average of 70.43. Dhoni was also the joint top-scorer in ODIs in 2009 along with Ricky Ponting, but the latter having played 30 innings. For his performances in 2009, he was named as captain and wicketkeeper of the World ODI XI by the ICC.
Dhoni scored two centuries in Sri Lanka's tour of India in 2009, a series of three matches in which he led India to a 2–0 victory. With this feat, India soared up to the number one position in Test cricket for the first time in history. India scored 726–9 (decl) in the third match of this series, which was their highest Test total then.
It was under his captaincy that India climbed to No. 1 in the ICC Test Rankings in December 2009. After that, India had clean sweep victories against Bangladesh and Australia. The series against South Africa, who are considered one of the best touring teams in the world, was drawn 1-1. India also came close to defeating South Africa in South Africa in early 2011 before Kallis' twin hundreds ensured that the series ended at 1-1.
As captain of the Indian cricket team, Dhoni has seldom been suspended due to his team's slow over-rate. In December 2009, he was suspended for two ODI matches against Sri Lanka by ICC match referee Jeff Crowe as India was three overs short of the specified rate; Virender Sehwag acted as captain for the two matches in Cuttack and Kolkata. In January 2012 Dhoni was banned for the fourth Test match against Australia in Adelaide as India was two overs short during the third Test in Perth. Sehwag captained the team in the Adelaide test and Wriddhiman Saha kept the wickets. In the CB Series in February, Dhoni again faced a one-match ban for slow over rate against Australia.