On being brought from Mumbai today, he was produced before a magistrate.
Pandi had been eluding arrest since January 31, 2013, after the murder of "Pottu" Suresh, a close aide Alagiri.
He shot to infamy after he was accused in the burning of the office of Tamil daily "Dinakaran" in 2007 in which three employees were killed. However, Pandi was acquitted in the case.
Several criminal cases, including kidnap, attempt to murder and land-grabbing, were pending against him.
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P Dhayal, wife of Pandi, had moved the petition contending that she apprehend that police might "kill him in fake encounter".
She contended that her husband had gone underground a couple of years ago only because of threat to life.
Claiming that she did not even know about his whereabouts for the last few years, Dhayal submitted that police had warned her of killing him if he continued to remain at large.
A division bench, comprising Justices S Nagamuthu and V S Ravi, dismissed the petition.