Agarkar was named the captain for the first four games.
Apart from Agarkar, the former Ranji Trophy champions will also miss another senior pacer in Zaheer Khan.
Zaheer, who turned out for the 39 times champions in the Ranji opener against Railways, will not available along with Sachin Tendulkar because of the upcoming four-Test series against England, commencing in Ahmedabad on November 15.
Agarkar has picked up a "minor" calf injury in the match against the Railways and has been advised a few days' rest, which ruled him out of the game against Rajasthan, said Mumbai Cricket Association's joint secretary Nitin Dalal today.
"Agarkar will be available for the subsequent games," said Dalal.
The trio has been replaced by Kshemal Waingankar, Shardul Thakur and Hiken Shah.
Mumbai have made another change in the team that played against Railways as Ajinkya Rahane, who scored a century and a half-century in his two innings in the opening game, is also a part of the Indian Test squad at Ahmedabad.
He has been replaced by Akhil Herwadkar.
The squad: Rohit Sharma (capt), Akhil Herwadkar, Ramesh Powar, Hiken Shah, Aditya Tare, Iqbal Abdullah, Suryakumar Yadav, Kshemal Waingankar, Dhawal Kulkarni, Shardul Thakur, Kaustubh Pawar, Ankit Chavan, Abhishek Nayar, Shoaib Shaikh. Coach: Sulakshan Kulkarni.
