The Anti-Terrorism Squad (ATS) submitted the 300-page document in which it has said Bhatkal was a key conspirator of the terror attack.
Three powerful blasts had ripped through crowded areas in Zaveri Bazar, Opera House and Kabutar Khana on July 13, 2011, killing at least 21 people and injuring 141.
"We have filed a chargesheet in the designated MCOCA Court today," Special Prosecutor Ujjwal Nikam told PTI.
The duo was arrested on February 5 by the ATS after a Delhi Court allowed its plea seeking their custody.
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Earlier, five accused - Naquee Ahmed, Nadeem Shaikh, Kanwar Pathrija, Haroon Naik and Mohammed Qafeel Ansari were held in the case and are facing trial under the stringent Maharashtra Control of Organised Crime Act (MCOCA), Indian Penal Code and other relevant laws.
The first chargesheet was filed a few months ago.
Those still wanted in the case are Riyaz Bhatkal, a top operative of IM, a home grown terror outfit, Waqas Ibrahim Sad, Dubai-based Muzaffar Kolah and Tehseen Akhtar Shaikh, the police said.
Yasin, who hails from Bhatkal village of Udupi district in North Karnataka, is also wanted in a string of terror attacks in Ahmedabad, Surat, Bangalore, Pune, Delhi and Hyderabad, the Central agency had said.
Yasin had been earlier associated with banned outfit SIMI.