While the reasons for his resignation are yet unclear, Rupani becomes the third BJP chief minister to step down in the recent past.
A probe will be conducted by a retired judge into the lathi-charge on August 28 and will also ascertain the role of IAS officer Ayush Sinha, who asked the police to 'break the heads' of farmers.
The bench was hearing a PIL filed by Lok Sabha MP from Madurai, Su Venkatesan, who approached the HC after he received a reply from the Centre in Hindi to a representation made by him in English.