Shami had been picked in the initial squad for the two tests, but was forced to withdraw due to fitness issues.
His replacement Avesh has not played a test match for India, but has featured in 19 Twenty20 internationals and eight one-day internationals, taking 27 wickets.
On Friday, India were also fined 10% of their match fee and docked two ICC World Test Championship points for maintaining a slow over rate in their innings and 32-run defeat to South Africa in the first test.
"Chris Broad of the ICC Elite Panel of Match Referees imposed the sanction after India were ruled to be two overs short of the target after time allowances were taken into consideration," cricket governing body ICC said.
India's test squad: Rohit Sharma (captain), Shubman Gill, Yashasvi Jaiswal, Virat Kohli, Shreyas Iyer, KL Rahul, Ravichandran Ashwin, Ravindra Jadeja, Shardul Thakur, Mohammed Siraj, Mukesh Kumar, Jasprit Bumrah, Prasidh Krishna, KS Bharat (wk), Abhimanyu Easwaran, Avesh Khan
