The AGP founder president defeated firebrand fellow MLA Padma Hazarika by 37 votes in a closely fought election during the day.
Mahanta secured 211 votes in the polls held at the AGP headquarters here while Hazarika bagged 174 votes, party spokesman Kamala Kalita told reporters here.
AGP's serving president Chandra Mohan Patowary had opted out of the fray citing lack of consensus.
Atul Bora (Junior), considered close to Hazarika, was elected working president of the party defeating Rajya Sabha MP Kumar Dipak Das, who was backed by Mahanta.
Bora secured 225 votes as against 157 votes by Das.
This is the first time that AGP is holding comprehensive organisational elections at all levels following recommendations of a panel headed by senior party leader Hitendranath Goswami.
Mahanta, who was president of All Assam Students' Union during the 1979-85 anti-foreigners agitation, had formed AGP along with his colleagues of the student body and signed the Assam Pact with the then prime minister Rajiv Gandhi.
Following it he had led AGP to a historic victory in the 1985 Assam assembly polls and became the youngest chief minister in the country at the age of 34.
He had served as chief minister from 1985 to 1990 and was leader of the Opposition from 1991 to 1996 when the state was ruled by the Congress. Mahanta donned the mantle of the chief minister for a second time from 1996 to 2001 when the party made a comeback in 1996 as part of a five party alliance. PTI PPB DG KK
