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Indian captain Rohit Sharma said the rule will hold back the development of all-rounders.
The writing was on the wall once Axar failed to recover on time for the third ODI against Australia in Rajkot.
Axar sustained multiple injuries during India's six-run loss to Bangladesh in their last Super Four match on Friday.
Surya suffered a freak injury during the match against Delhi Capitals.
The 36-year old Warner steps in as skipper for injured Rishabh Pant, who is currently undergoing rehab and recovery after surviving a horrific car crash last year.
The hosts finished a run behind Australia's 263 and the latter were 61/1 at stumps on day two.
Australia, who conceded a mammoth 223-run lead, were bowled out for a paltry 91 in their second innings.
After going wicketless in the opening session, Indian bowlers picked six wickets in the remaining two sessions on the fourth day.
The all-rounder is expected to be out of action for at least three months.
The team management would hope for a quick recovery of Jadeja ahead of the T20 World Cup in Australia in October-November.
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