Besides the seers, arraigned as accused 1 and accused 2 respectively in the murder of A Sankararaman, Manager of the Varadarajaperumal temple in Kancheepuram district, 21 other accused were also acquitted by Puducherry Principal District and Sessions Judge C S Murugan.
A total of 24 persons were made accused in the case, but one of them, Kathiravan, was killed early this year.
Also Read: Chronology of events in Sankararaman case
The judge held that the witnesses failed to support the prosecution case that the two Sankaracharyas -- Jayendra (78) and Vijayendra (44) -- were part of a conspiracy to eliminate the temple official in September 2004.
He also said the witnesses, including Sankararaman's daughter, failed to identify the accused in the court. None of them identified any accused in the court and no incriminating evidence was made out against the accused, the judge noted.
The arrest of Jayendra Saraswathi on Diwali day in November 2004 in Andhra Pradesh and later his heir apparent, Vijayendra, came as a big jolt to the Kanchi Mutt and its followers.
During the trial, 189 witnesses were examined between 2009 and 2012, of which 83 turned hostile.
The keenly-anticipated judgement was delivered in a packed court hall for which security was beefed up in and around the area.
Sankararaman, who was murdered in his office room in the temple on September 3, 2004 using sharp-edged weapons, had levelled charges of financial misappropriation against the two Sankaracharyas and over the way they ran the Mutt.
Police from Vishnukanchi station took up investigation following a complaint and a case was registered under section 302 and 34 of Indian Penal code.
Cases were registered against the two seers under section 120-B (criminal conspiracy) and 302 (murder) of IPC in connection with the murder.
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