He was being treated for age-related illnesses in Chennai (formerly Madras) in southern India's Tamil Nadu state.
Mr Karunanidhi served as the chief minister of Tamil Nadu five times between 1969 and 2011, and also played a key role in federal politics.
Police have increased security amid fears of unrest among his supporters, who have gathered in the streets.
Mr Karunanidhi died at 18:10 local time (13:10 GMT), the Kauvery Hospital in Chennai said.
He was active in politics until his death and most recently contested the 2016 state assembly against his long-time opponent and bitter rival Jayaram Jayalalitha, who died later that year.
An atheist and self-declared rationalist, Mr Karunanidhi rose to political prominence in the 1940s as part of the Dravidian movement - which challenged the caste supremacy of Brahmins - and through his participation in anti-Hindi language agitations.
A prolific writer and a fiery speaker known for his wit and oratory, he enjoyed god-like status among his supporters.