Mr Bachegowda had lost 2018 assembly polls by over 7,000 votes.
The Ruling BJP in Karnataka on Thursday expelled from its primary membership rebels Sharath Bachegowda and Kaviraj Urs, contesting the coming assembly bypolls as independent candidates, for anti-party activity.
In separate letters to both Sharath Bachegowda fighting from Hoskote assembly constituency, and Urs fighting from Vijayanagara, BJP said, their contest against the party's official candidate was being considered as anti-party activity.
BJP on Wednesday had asked the party rebels to withdraw their candidature by Thursday, the last day for the process.
The BJP gave the Hoskote ticket to disqualified Congress legislator MTB Nagaraj, however, Mr Bachegowda jumped into the fray as an independent.
The JD(S), meanwhile, decided to support him and has not fielded a candidate.
Mr Bachegowda had lost 2018 assembly polls by over 7,000 votes.
On the other hand, Mr Urs filed his nomination as an independent candidate from Vijayanagara, rebelling against party's decision to field Anand Singh, another disqualified MLA.
The party's decision to expel Urs comes after repeated attempts to "pacify" him.
The BJP has fielded 13 of the 16 disqualified legislators, who joined the party, as its candidates from their respective constituencies in the bypolls.