The apex court on July 1 protected Setalvad from arrest and stayed for a week the high court order rejecting her plea for regular bail and asking her to surrender immediately.
In a special late-night hearing, a Supreme Court bench of Justices B R Gavai, A S Bopanna and Dipankar Datta questioned the denial of time to Setalvad to appeal against the HC order.
The court of Justice Nirzar Desai rejected Setalvad's bail plea and directed her to surrender immediately as she is already out of jail after securing interim bail.
In February 2002, 59 people were killed when a coach of the train was burnt at Gujarat's Godhra, triggering riots in the state.
Notorious former VHP leader Babu Bajrangi has also been acquitted.
Pinarayi Vijayan tweeted a tribute to Ehsan Jafri, on the 21st death anniversary of the former Congress leader.
The prosecution was unable to gather enough evidence against the accused persons, and even witnesses turned hostile, defence lawyer Gopalsinh Solanki said.
It is 'censorship', says the MP; Congress claims Modi is scared of the 'truth of 2002'.
The judge who convicted the 11 men 14 years ago was unhappy with the distasteful reception accorded to them.
'I trusted the system, and I was learning slowly to live with my trauma,' said the survivor, who was gangraped and her seven family members were murdered in post-Godhra riots.