Delivering the verdict, the Special Maharashtra Control of Organised Crime Act (MCOCA) Judge Yatin D Shinde held 12 of the 13 accused guilty while acquitting one of them.
The convicts were allegedly linked to the banned Students Islamic Movement of India (SIMI).
The accused were found guilty of charges under IPC, Explosives Act, Unlawful Activities Prevention Act, Prevention of Damage to Public Property Act and Indian Railway Act and those under MCOCA.
Those convicted today are Kamal Ahamed Ansari (37), Tanvir Ahmed Ansari (37), Mohd Faisal Shaikh (36), Ehtesham Siddiqui (30), Mohammad Majid Shafi (32), Shaikh Alam Shaikh (41), Mohd Sajid Ansari (34),Muzzammil Shaikh (27), Soheil Mehmood Shaikh (43), Zamir Ahmad Shaikh (36), Naveed Hussain Khan (30) and Asif Khan (38).
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During the investigations, 13 accused, all of them Indians, were arrested and brought to trial.The chargesheet filed by Anti Terrorism Squad (ATS) in November 2006 had named 30, 17 of them absconding and out which 13 are said to be Pakistan nationals.
Arguments for the quantum of sentence are likely to begin on Monday.
The ATS chargesheet had said that Improvised Explosive Devices (IEDs) were made in a room in Govandi in suburban Mumbai and some Pakistani nationals were also present during the bomb-making.
Seven RDX bombs had exploded in the first class coaches in many suburban trains on July 11, 2006, killing 188 people and injuring 829.
In the trial that ran for eight long years, the prosecution examined 192 witnesses, including eight Indian Police Service (IPS) and five Indian Administrative Service (IAS) officers as well as 18 doctors. The defence lawyers examined 51 witnesses and one person was called as a court witness.