A review of the apex court's ruling last month had been sought by the federal government, rights groups and the LGBT community.
A Supreme Court bench of Justices H.L. Dattu and S.J. Mukhopadhaya, however, dismissed the review petitions, the Times of India reported.
In its ruling last month, the high court had set aside a 2009 New Delhi lower court order decriminalizing sex between consenting persons of the same sex and upheld Section 377 of a 19th century law, which says sexual acts between members of the same sex are "against the order of nature." The high court acted on appeals by various social and religious organizations that maintain gay sex is against the cultural and religious values of the country.
The high court, without taking a stand, said the New Delhi lower court order cannot be constitutionally sustained as only Parliament can change the current law.
Since the December ruling, gays have said their fundamental rights have been violated.
In their review petitions, gay rights activists, including the non-governmental organization Naz Foundation, also said thousands from the LGBT community had come out openly about their sexual identity since the 2009 New Delhi court order, but could now be threatened with prosecution, the Hindustan Times reported.
The activists said there were a number of "grave errors of law" and "wrong application of law" that need correcting.
The federal government also filed a petition amid widespread outrage bout the Supreme Court's December ruling, saying a review was needed to "avoid grave miscarriage of justice to thousands of LGBT."
NDTV quoted rights activists as saying they are extremely disappointed in Tuesday's development and they would file another petition.