The 38-year-old Dhoni, who skipped the team's ongoing tour of the West Indies due to military duty, is not part of the 15-man squad for the games starting September 15 in Dharamsala.
Fit-again all-rounder Hardik Pandya is the only change from the squad that white-washed the West Indies in three T20 games early this month.
Youngster Rishabh Pant is being groomed to take over from Dhoni as the team's first-choice gloveman.
Dhoni, who led India to their 2011 World Cup triumph on home soil, faced criticism for his poor form and ponderous style of batting at the World Cup in England and Wales earlier this year.
But selectors and pundits backed Dhoni to make his own choice as the former captain, an honorary lieutenant colonel in a reserve force, decided to serve in the military.
Dhoni gave up Test cricket in 2014 but remained India's mainstay in the limited-overs formats and is often seen as a key aide to current skipper Virat Kohli.
Kohli's India will also play three Test matches against the visiting South Africans in October after the T20 matches.
India squad
Virat Kohli (capt), Rohit Sharma, Shikhar Dhawan, KL Rahul, Shreyas Iyer, Manish Pandey, Rishabh Pant (wkt), Hardik Pandya, Ravindra Jadeja, Krunal Pandya, Washington Sundar, Rahul Chahar, Khaleel Ahmed, Deepak Chahar, Navdeep Saini