He will be replacing G Ramakrishnan.
Balakrishnan was elected on the concluding day of the party's three-day state conference in Tuticorin today, a CPI(M) release here said.
The state conference was attended by among others, party General Secretary Sitaram Yechury and his predecessor Prakash Karat.
Balakrishnan joined CPI(M) in 1970 as a student and rose through the party ranks.
He was active in various areas, including farmers' and workers' rights, the release said, adding he lived 'underground' during the Emergency.
He had represented Chidambaram as MLA during the 2011-16 period.