The move is seen as an apparent quid pro quo for sacking jailed leader VK Sasikala and himself.
Ms Sasikala was sacked as interim chief at the meeting of the executive committee and general council, the party's top decision making bodies, on Tuesday.
Also, all appointments made by her, including that of naming Mr Dhinakaran as deputy chief, were rescinded.
Against this backdrop, Chief Minister K Palaniswami, who is the Headquarters Secretary, was removed from his post.
In his place, former Minister and sitting MLA P Palaniappan, a key Mr Dhinakaran loyalist, was named the party's Headquarters Secretary, a party release said.
It may be recalled that Mr Palaniswami was removed from his another post of Salem Suburban District Secretary last month following the merger of Mr Palaniswami and O Panneerselvam factions.
At that time, there was no mention whether Mr Palaniswami continued to hold his key post of headquarters secretary.
In another major move, Mr Dhinakaran removed Forest Minister Dindigul C Srinivasan from his post as party treasurer.
Mr Srinivasan was named treasurer by Mr Sasikala before she surrendered in a Bengaluru court on February 15 following her conviction in a graft case.
Sitting MLA (Thanjavur) M Rengasamy replaces Mr Srinivasan as party treasurer.
Mr Dhinakaran, meanwhile, in another party release dated "September 11" and issued on Wednesday, announced the removal of two more senior functionaries from their posts.
Tamil Nadu government's Special Representative in Delhi, N Thalavai Sundaram and chairman of Tamil Nadu Wakf Board A Tamilmahan Hussain were removed their respective party posts.
While Sundaram is the party's organising secretary and also a former State Minister and an ex-Rajya Sabha MP, Tamilmahan Hussain is the Secretary of Anaithulaga MGR Mandram, a party wing.
The move comes after the removal of many party functionaries from their respective posts as they had sided with Chief Minister Palaniswami and Panneerselvam camp.