The Centre had earlier told the high court that marriage between same sex couples was "not permissible" as it was not recognised by "our laws, legal system, society and our values".
A Bench headed by Justice Ashok Bhushan dismissed an appeal filed by petitioner Himanshu Agarwal against a December 2019 order of the Bombay High Court.
One Vikram Gehlot had filed the PIL seeking dismissal of the government alleging that the affairs of the state were not being carried out in line with constitutional and legal provisions.