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The 29-year-old Rahul has played 40 Tests so far and has scored 2,321 runs at an average of 35.16 with six centuries under his belt.
The three-match series starts with the Boxing Day Test in Centurion.
Azhar pointed out that the absence of Rohit from the Test series and Kohli's break from the ODI series will lead to unnecessary speculation about rift in the squad.
It is learnt that Kohli has already informed the BCCI about his decision.
Rohit sustained a left hamstring injury during his training session in Mumbai on Sunday.
The reasoning given by the BCCI that Rohit Sharma was appointed as captain in order to have one leader for white- ball cricket is a specious one.
The BCCI chief said that once Virat Kohli refused to continue as India's T20I captain, the selectors made up their mind to hand the ODI reins to Rohit Sharma.
Rohit has been impressive with his tactics and calm demeanour, but full-time captaincy will be a different challenge altogether.
Ajinkya Rahane was removed from Test vice-captaincy, a position which was also given to Rohit.
The Indian Test squad for the tour of South Africa will be announced on Wednesday.