Off-spinner Harbhajan Singh, who played the last of his 229 one-dayers in June 2011, returns to the 15-member side for the world number two ODI team's series against a Zimbabwe team ranked nine places lower.
Apart from Dhoni, Virat Kohli, Suresh Raina, Rohit Sharma, Shikhar Dhawan and Ravichandran Ashwin have also been rested after India's disappointing tour of Bangladesh where they lost the three-match ODI series 2-1.
"We are confident of Ajinkya's ability (to lead) and want him to do well," chief selector Sandeep Patil told reporters in New Delhi.
"We're very happy the way his career is shaping up. He is one of the most consistent batsmen we have," Patil said of the 27-year-old who has played 55 ODIs since his 50-overs debut in 2011.
"That's why we want to see his other aspects. We have given him this opportunity and we'll definitely back him," said Patil, insisting the team was chosen with an eye on next year's Twenty20 World Cup in India.
The team does not include any specialist glovesman but contains three batsmen -- Robin Uthappa, Kedar Jadhav and Ambati Rayudu -- who can keep wickets.
Manish Pandey and Sandeep Sharma are the uncapped players in the ODI side.
Harare Sports Club hosts the ODIs on July 10, 12 and 14, to be followed by Twenty20 Internationals on July 17 and 19 at the same venue.
Team director Ravi Shastri will not tour Zimbabwe either, Indian cricket board secretary Anurag Thakur said.
The board would meet next month to discuss who would succeed Duncan Fletcher as the new head coach, he added.
Squad: Ajinkya Rahane (captain), Murali Vijay, Ambati Rayudu, Manoj Tiwary, Kedar Jadhav, Robin Uthappa, Manish Pandey, Harbhajan Singh, Axar Patel, Karn Sharma, Dhawal Kulkarni, Stuart Binny, Bhuvneshwar Kumar, Mohit Sharma and Sandeep Sharma
(Reporting by Amlan Chakraborty in New Delhi; editing by Sudipto Ganguly)
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