The 80-year-old pontiff and others were accused of ordering an attack on the temple auditor S Radhakrishnan in September 2002.
The auditor was attacked by a gang at his Chennai residence and the prosecution had claimed it was an attempt to murder.
The prosecution had alleged the attack was carried out on orders by the senior pontiff as he suspected the auditor of filing complaints against his administration and raising questions about purported irregularities in the Kanchipuram Mutt.
This is the second major reprieve for the Kanchi Sankaracharya. In November 2013 a court in Puducherry acquitted him and the junior Pontiff Vijeyandra Saraswathi in a murder case.
The temple manager Sankararaman had exposed alleged malpractices and misuse of funds at the mutt.
The arrest of the pontiffs during Tamil Nadu Chief Minister J Jayalalithaa's earlier tenure had triggered criticism.
Recently BJP President Amit Shah took a tacit dig at her in Chennai saying, "tough action" against Kanchi mutt pontiffs was "politically motivated".
In the verdict on Friday, eight of the eleven accused have been acquitted.
Two of the accused have already died and one had turned approver.
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