Warner suffered a fractured elbow during the second Test defeat in Delhi last week, a game he was forced out of on day two after also failing a concussion test.
The 36-year-old, who scored just 26 runs in three innings in the series, will follow seamer Josh Hazlewood in having his tour curtailed by injury, while captain Pat Cummins has also flown home for personal reasons but is due to return in time for the third Test, which starts on March 1.
In Warner’s absence, Travis Head opened the batting in the second innings in Delhi and is expected to do likewise in Indore, with all-rounder Cameron Green expected to be fit to return at No6 having yet to feature in the series.
Australia’s hopes of regaining the Border-Gavaskar Trophy are already over after India raced into a 2-0 series lead inside six days of cricket.
The tourists were thrashed by an innings and 132 runs in the first Test in Nagpur and then lost nine wickets in a session to blow any chance of levelling the series, having so far had no answer to the twin spin threat of Ravi Ashwin and Ravi Jadeja on turning pitches.