The star batsman had said he would only play in Dharamsala if fully fit, but was left out of the team on Saturday.
Kohli’s absence is a huge blow to India, whose series against Australia is locked at 1-1 ahead of the decider.
However, Kohli has struggled throughout, making just 46 runs at an average of 9.20.
Ajinkya Rahane will captain India, with debutant spinner Kuldeep Yadav taking Kohli’s place in the XI.
Bhuvneshwar Kumar replaces Ishant Sharma in India’s only other alteration. Australia are unchanged.
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