With Virat Kohli excusing himself from the series because of personal reasons, India would have been hoping for Rahul to regain full fitness after being ruled out of the second Test in Visakhapatnam.
But while a Board of Control for Cricket in India statement revealed Rahul had "reached 90 per cent of match fitness and is progressing well", the hosts are unwilling to take any risks over the 31-year-old.
Devdutt Padikkal, whose international career so far has comprised of two T20s, has therefore been named as a replacement for Rahul ahead of the series, which is evenly-poised at 1-1, resuming on Thursday.
Rahul has amassed eight hundreds in 50 Tests and was widely expected to slot back in at number four - where he made 86 and 22 in the series opener - after selectors axed the misfiring Shreyas Iyer.
Rahul will now continue his rehabilitation under the supervision of India's medical staff in Bengaluru with a view to being welcomed back for the fourth Test in Ranchi, which gets under way on February 23.
Padikkal, meanwhile, joins a middle-order mix also containing another uncapped batter in Sarfaraz Khan while Rajat Patidar only came in for his Test debut in Vizag.
It is unclear whether highly-rated all-rounder Ravindra Jadeja can bolster the batting after a hamstring problem precluded his involvement in India's series-levelling win last time out.