Mr Pandian had a stelar record and he was the "main" officer who had taken on fugitive gangster Dawood Ibrahim and the ISI of Pakistan when he was with the IB, senior advocate Mahesh Jethmalani, his lawyer, told the court.
The Central Bureau of Investigation, which took over the encounter case from the Gujarat CID in 2010, framed Mr Pandian by fabricating evidence, he alleged.
"I (Pandian) have unimpeachable documentary evidence to prove that I was not in Hyderabad on the day of the alleged abduction," Mr Jethmalani contended in the court.
As per the CBI, Sohrabuddin, a gangster with alleged terror links, his wife Kausar Bi and his aide Tulsiram Prajapati were abducted by the Gujarat police on the night of November 22-23, 2005 while they were travelling from Hyderabad to Sangli in a private bus.
"I had taken a flight from Hyderabad to Ahmedabad on November 23, 2005.... However, the CBI claims I never took that flight and instead sent constable Ajay Parmar to Ahmedabad on my ticket as a cover-up," the lawyer said.
It was an international flight of Air India, where every passenger's ID card would have been checked, he said.
The CBI presented, as evidence, the custom declaration form submitted at the Hyderabad airport, filled in Pandian's name but bearing Parmar's signature, Mr Jethmalani said.
The agency claimed that it proved that Parmar took the flight on Mr Pandian's ticket to help him cover his tracks. "This is a fabricated document. I am a victim.... The victim of false investigation by the CBI," Mr Jethmalani said.
"I was the main officer who fought Dawood Ibrahim and ISI (during a stint as SP with the Intelligence Bureau). I have an unimpeachable record, and yet, the CBI is trying to undermine me like this," the lawyer said.
According to Mr Pandian, he was in Hyderabad on November 21-22, 2005 only to inspect the site of a bomb blast that had taken place near the city in October that year, and he had nothing to do with the alleged abduction of Sohrabuddin.
Sohrabuddin and Kausar Bi were killed in an alleged fake encounter by the Gujarat police in November 2005, while Prajapati was killed in another alleged fake encounter by the Gujarat and Rajasthan police in December 2006.
Of the 38 persons charge-sheeted by the CBI for being involved in the two fake encounters, 15, including senior IPS officers D G Vanzara, Pandian, Dinesh MN, and BJP president Amit Shah were discharged by the special CBI court in Mumbai, where the trial is underway.
The high court is conducting day-to-day hearing on petitions filed by the CBI and Rubabuddin Shaikh, Sohrabuddin's brother, challenging the discharge of five of the 14 police officers.