Asghar Ali was brought here by the Central Bureau of Investigation (CBI) from Hyderabad where he was lodged in a jail in an another case.
Pandya was the home minister in then Narendra Modi-led Gujarat government. He was shot dead on March 26, 2003, near Law Garden in Ahmedabad while he was out for a morning walk.
Special Judge for Prevention of Terrorism Act (POTA) M K Dave remanded him in judicial custody.
Last month, eight other convicts in the murder case were sent to jail by the court following their surrender.
Since Ali was in Hyderabad jail, the CBI secured his warrant and brought him here on Thursday.
The Supreme Court had restored the conviction of 12 people in the case. Ali and eight others are now behind bars while three have completed their sentence.
The Apex Court on July 5 this year, set aside the Gujarat High Court’s decision which had absolved the accused of murder charge.