Thakur suffered an injury to his left shoulder while dropping a catch on the opening day of Mumbai's last league game against Tripura which the hosts won by 10 wickets at the Wankhede Stadium here.
Even Shreyas Iyer, who has been picked in the Indian side for the ODI series against Sri Lanka, has not been included in the squad.
The squad, to be led by Aditya Tare, includes their in-form young batsman Prithvi Shaw and opener Jay Bista.
Other regulars - Akhil Herwadkar, Siddesh Lad, Surya Kumar Yadav, senior pro Dhawal Kulkarni, medium pacer Akash Parkar and left-arm spinner Karsh Kothari - have all been named in the squad.
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The domestic cricket powerhouse stormed into the quarterfinals after a comprehensive win over Tripura.
The 41-time Ranji Trophy champions will lock horns with Karnakata in Nagpur for a place in the semifinals.
Squad: Aditya Tare (Captain), Surya Kumar Yadav (Vice Captain), Dhawal Kulkarni, Siddhesh Lad, Jay Bista, Prithvi Shaw, Akhil Herwadkar, Sufiyan Shaikh, Akash Parkar, Karsh Kothari, Sagar Trivedi, Vijay Gohil, Shivam Malhotra, Shivam Dube and Shubham Ranjane.
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