The party's official twitter handle earlier carried its poll symbol 'hand' as the profile picture.
The move came a day after Thakur, an accused in the Malegaon blasts, described Mahatma Gandhi's assassin Nathuram Godse as a "deshbhakt" (patriot). "Nathuram Godse was a 'deshbhakt', is a 'deshbhakt' and will remain a 'deshbhakt'. People calling him a terrorist should instead look within. Such people will be given a befitting reply in these elections," she had said.
The Bharatiya Janata Party's (BJP) Anant Kumar Hegde and Nalin Kateel have also praised Godse as they came out in Thakur's support.
Earlier in the day, BJP President Amit Shah said that the statements made by Thakur, Hegde and Kateel were their personal comments and that the party had nothing to do with them.
"However, they have retracted their statements and have also apologised. The BJP has taken a decision to send their statements to the party's disciplinary committee. The committee will submit a report within 10 days after receiving the replies of the three leaders over their statements that are against the ideology of the party," Shah said.
The BJP President's announcement came as the party faced criticism over the controversial remarks ahead of the final phase of Lok Sabha elections.
Godse shot dead Mahatma Gandhi at a prayer meeting in New Delhi on January 30, 1948. He was hanged after a trial.