He replaced Udhayakumar with MLA S Mariappan Kennedy, a loyalist.
He also removed V V Rajan Chennappa, MLA, as party Madurai urban secretary, a statement said.
Dhinakaran, nephew of V K Sasikala, also appointed some of his supporters to various party posts, two days after the merger of the two factions led by Palaniswami and rebel leader O Panneerselvam, a former chief minister.
Dhinakaran had dubbed the merger as a "betrayal" of party general secretary Sasikala.
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The move came a day after Vaithilingam, a Palaniswami loyalist, said steps would be taken for the removal of Sasikala from the AIADMK.
MLAs loyal to Dhinakaran had told Governor Ch Vidyasagar Rao they have lost confidence in Chief Minister EK Palaniswami.
The MLAs are currently camping at a resort in neighbouring Puducherry.
The main opposition DMK has demanded a floor test in view of the rebellion in the AIADMK.