Parag Sawant, 36, whose wife was pregnant with their daughter when he was admitted, spent two years in a coma and was then in a semi-conscious state, his doctor told PTI news agency.
On 11 July 2006 one of seven bombs exploded in his train carriage.
The bombings killed at least 187 people and injured more than 800, PTI said.
The bombs were packed into seven pressure cookers and put in bags during the evening rush hour.
"He was in a deep coma for about two years and then his condition gradually improved into a semi-conscious state where he would understand simple commands," neurosurgeon BK Misra said.
Mr Sawant died when his lungs and heart stopped and he could not be resuscitated.
In 2010 when  he came out of the coma, his wife Preeti told The Hindu newspaper: "He recognised me, our daughter. I am very happy."
The paper reported his wife had been given a job in the Western Railway and officials had paid for medical fees.
He was visited by Sushma Swaraj, then leader of the opposition in parliament, who criticised the government for the lack of prosecutions in the case.
Indian militants were blamed for the attack.
NDTV reports the case has now concluded, with 13 tried, but a court in Mumbai is yet to give its verdict.
An Indian man has died after spending nine years in hospital with severe brain injuries suffered in the 2006 bombing of commuter trains in Mumbai.