The judgment was delivered by Puducherry Principal District and Sessions Judge C.S. Murugan in the trial that was spread over nine years.
The judge said the witnesses were not able to support the prosecution case of murder conspiracy against the two seers.
Both the seers were present in the court when the judgement was delivered. Immediately on hearing the verdict, the two seers left the court premises.
Speaking to reporters, counsel for the two seers said the prosecution has not proved the charge of conspiracy behind the murder.
The wife, son and daughter of Sankararaman were also not able to identify the murderers.
Counsel added this is not a fit case for appeal in the higher court for the government.
A. Sankararaman, who worked as a manager in the Varadarajaperumal temple in Kanchipuram in Tamil Nadu, was murdered inside his office in the temple Sep 3, 2004.
According to police, Sankararaman was writing complaint letters to the Mutt under a pseudonym about financial misappropriation.
The two seers of Sankara Mutt in Kanchipuram - Jayendra Saraswathi and Vijayendra Saraswathi - were cited as accused number one and two.
Tamil Nadu Police arrested Jayendra Saraswathi in Andhra Pradesh on Diwali day in 2004, shocking not only the followers of the Kanchi Sankara Mutt but also Hindus in general.
One of the accused, M. Kathiravan was murdered in March this year here.
There were 22 other accused, including manager of Sankara Mutt N. Sundaresan, and Jayendra Saraswathi's brother M.K. Raghu.
All the 24 were charged under various sections of the Indian Penal Code for criminal conspiracy, abetment to the crime and other crimes.
The case trial was shifted to Puducherry from a Chengalpet court near here on the petition from Jayendra Saraswathi, the senior seer, after he complained that the atmosphere in Tamil Nadu was not right for a free and fair trial. The Supreme Court then allowed the trial to be shifted to Puducherry in 2005.
The apex court also directed the Puducherry government to appoint its own public prosecutor on a petition from Jayendra Saraswathi.
For the trial, 189 witnesses were examined between 2009 and 2012. Interestingly, 83 of them turned hostile. Even the approver, Ravi Subramaniam, turned hostile and denied his earlier statements to police.
The prosecution also examined Padma, wife of Sankararaman, and their son Anand Sharma and daughter Uma Maithreyi.
Welcoming the acquittal Ambur Jai Shankar, president, Vijaya Bharatham Makkal Katchi, told IANS: "Justice has won. Hindus all over the world will be happy now."
He said the police can re-investigate the case to find the real culprit.
Arjun Sampath of Hindu Makkal Katchi told IANS: "Dharmathin vazhu thanai soodhu kavvum, irudhiyil dharmam vellum (Dharma may seem to lose initially to conspiracy but in the end dharma will triumph)."
He said the case was mainly to target the organisation that was revered and kept on high pedestal by Hindus.
"Several anti-Hindu organisations and media threw mud at the Mutt. Now they will have to answer," Sampath added.
Several people assembled at the court premises to hear the judgment. Soon after hearing the verdict, the people shouted slogans in support of the two seers.
--IANS (Posted on 27-11-2013)