Warner made a scratchy 15 in Australia's first innings of 263 and was struck on the helmet by Indian paceman Mohammed Siraj.
He did not field when India batted for nine overs on Friday evening and later failed a concussion test.
Warner was also hit on the elbow from Siraj delivery earlier in his 15-over stay at the crease, requiring immediate attention from medical staff.
He has been replaced in Australia's XI by Matt Renshaw, who has dropped for the recalled Travis Head after twin failures with the bat in the opening Test in Nagpur.
It is the second time Australia have been forced to use a concussion sub mid-match after Steve Smith was replaced by Marnus Labuschange during the 2019 Ashes after being hit on the head by a Jofra Archer bouncer.
Warner's position in the Test team was already under a cloud after being down on form for the majority of the last three years.
The aggressive left-hander entered the Boxing Day Test in December - his 100th match - under extreme pressure to retain his spot.
But Warner scored a classic 200 to to end a near Test century drought dating back to January 2020 to book his spot for a third red-ball tour of India.
Warner's Test record in India is dismal, averaging 21.78 there.
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