The funeral service was led by top priests of the Catholic Church.
Thousands of people assembled at his residence and the Church paid tributes to Mani, who died at a private hospital in Kochi Tuesday at 86.
Former chief ministers A K Antony and Oommen Chandy, Leader of Opposition in the State Assembly Ramesh Chennithala, Kerala Congress (B) chairman R Balakrishna Pillai and IUML leader P K Kunhalikutty were among those who paid their last respects at Mani's residence when his body was brought Thursday morning.
AICC general secretaries K C Venugopal and Mukul Wasnik also paid tributes.
Assembly speaker P Sreeramakrishnan, veteran CPI(M) leader V S Achuthanandan, ministers Kadannappally Ramachandran and E Chandrasekharan paid homage when the procession reached Kaduthuruthy Wednesday evening.
Mani's body was kept at Thirunakkara Maithanam in Kottayam and his village Marangattupalli before being taken to his residence at Pala at around 7 am Thursday.
Thousands lined the route when the body was taken from the residence to the Cathedral.
Mani died at a private hospital in Kochi on Tuesday evening while undergoing treatment for pulmonary disease.
The Kerala Congress(M) leader had been the MLA of Pala for 54 years without a break till his death.
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