Sentencing came to a halt last month after the defence appealed against the validity of the trial which is being held under a defunct anti-terrorism law.
However, last week, Judge PD Kode rejected the plea and resumed sentencing on Tuesday, jailing the two men for conspiracy.
One of them, Imtiaz Gawate, was also found guilty of planting a bomb in a scooter, which did not go off due to a faulty fuse.
"These are serious crimes, but he is found to be affected with a very serious disease, HIV," said Kode.
"The prosecution, in view of this, did not press for the death sentence," he said, adding that Gawate had avoided capital punishment also because the bomb had not gone off.
The judge found the second man, Nasim Ashraf Bharmare, guilty of throwing a hand grenade at a stationary aircraft at Mumbai airport. No one was injured in that explosion.
Police say the bombings of several Mumbai landmarks, including the stock exchange, were ordered by Dawood Ibrahim to avenge the razing of an ancient mosque by Hindu zealots in 1992.
Bollywood star Sanjay Dutt is the most high-profile convict. He was found guilty of illegal possession of arms and could face up to 10 years in jail. His sentencing is likely next week.