The Mumbai court on Tuesday found three other members of the Memon family accused in the case not guilty.
The verdicts against the remaining 116 defendants, including Bollywood star Sanjay Dutt, will be handed down in batches in the coming weeks.
Sentencing will be announced after all the verdicts are delivered.
The court had been due to deliver its judgment last month but put it off until Tuesday.
The series of 13 blasts in the country's financial hub, with targets including the Bombay Stock Exchange building, a cinema hall and a busy market, were the deadliest bomb attacks in Indian history.
The trial, held in a court located inside a prison complex for security reasons, opened in 1994, but hearings began in earnest only the following year.
A total of 686 witnesses have been heard over more than a decade.
The serial blasts rocked Mumbai,
the country's financial hub
Of the 123 defendants, 11 died during the trial, 36 are in jail and the rest are out on bail. Another 37 suspects, including Ibrahim, have been declared "absconders" or fugitives.
Most prominent of the defendants is Dutt, arrested after two suspects said he had bought an assault rifle from them. The actor was freed on bail after more than a year in prison.
Indian authorities say Dawood Ibrahim, an alleged Mumbai criminal who they believe is now living in Pakistan, masterminded the attacks in retaliation for the destruction of a 16th-century mosque by Hindus.
Ibrahim and his associates never faced trial, having fled the country soon after the blasts, investigators say.
The Memon family was charged with organising and carrying out the attacks.
Investigators say that Ibrahim, a Muslim, may have been influenced by Pakistan.
They say the bombings were substantially funded from abroad but no clear links to Pakistan have been established.
New Delhi has repeatedly asked Islamabad to hand over Ibrahim and his associates. Pakistan denies they are on its territory.