Arriving here by a special flight, Modi reached the government estate and paid his respects to the late former Chief Minister of Tamil Nadu.
After going around the casket in which the body was wrapped in the tri-color, the Prime Minister patted M.K. Stalin, Karunanidhi's son and political heir, and his daughter Kanimozhi, MP, and comforted them with words of solace.
After exchanging a few words with them, Modi also comforted other family members and left the place.
Modi, in November last year, visited the Gopalapuram residence of Karunanidhi and urged him to come to the Prime Minister's official residence in Delhi for medical care if he wanted.
Though the Prime Minister's visit was acknowledged as a political nicety in deference to the senior-most political leader of the country, observers also feel it could send signals to the DMK ahead of the 2019 Lok Sabha elections in the state where uncertainty clouds political scene.
The Prime Minister was accompanied by Tamil Nadu Governor Banwari Lal Purohit, Defence Minister Nirmala Sitharaman, Union Minister Pon Radhakrishnan and state BJP President Tamilisai Soundararajan. Sitharaman also comforted Stalin and Kanimozhi.
Modi also greeted with folded hands the crowd of mourners who shouted to acknowledge his atrrival. Stalin and other DMK leader saw him off.