Two of the other four judges on the bench agreed with Justice Chandrachud on the court not legalising same-s£x marriages, making it a majority.
Two of the judges had supported same-s£x unions.
Abhijit Ghosh, a 45-year-old gay man and graphic designer from the western Indian city of Ahmedabad said he was “disappointed” about the verdict.
Mr Ghosh said he has kept the relationship with his partner secret for more than five years and legalising same-s£x marriage would mean that he could disclose his relationship to his parents.
“I could have told my family that my relationship has been recognised by Indian law, so my family could have a second opinion about accepting myself and my partner,” he said.
The petitioners had said validating same-s£x marriage would help them access some of the legal benefits of matrimony, including adoption, insurance and inheritance.
“Now we don’t have any legal rights, the relationship cannot have any future,” Mr Ghosh said.
“For example, if something happens to me, my partner cannot make a [medical] decision on my behalf … certain things have to be legally recognised.
“If those rights are given to us, my family would have been more acceptable [of the relationship],” Mr Ghosh said.
The court ruling comes five years after a historic 2018 judgement by the Supreme Court that scrapped a colonial-era ban on g@y s£x.
A five-judge bench headed by Chief Justice DY Chandrachud heard arguments in the case between April and May this year and pronounced its verdict on Tuesday.
Advocates representing nearly two dozen petitioners said it was time for India to treat the country’s LGBTQ community as equal citizens under its constitution.
Marriages in India are governed by family laws for specific religions, such as the Muslim Marriage Act and the Hindu Marriage Act.
The judges have been considering whether the Special Marriage Act of 1954 — which allows marriages between people of different castes and religions — could be expanded.
Despite the verdict on same-s£x marriage, the court said the country had a duty to acknowledge LGBTQ relationships and to protect them from discrimination.
“Our ability to feel love and affection for one another makes us feel human,” Justice Chandrachud said.
“This court has recognised that equality demands that queer unions and queer persons are not discriminated against.”
Ankit Bhuptani, a 31-year-old gay rights activist from the western Indian city of Mumbai, said despite the disappointment on the same-s£x marriage verdict, there were “many small, small positive aspects” from the court ruling.
“Like non-discrimination, setting up shelter home for LGBTQ people, and recognising diversity and gender identity as they are,” he said.
“I think I’m the luckiest queer generation in India, because the generation fights for the struggles and values freedom the most.
“We are talking about recognising of same-gender relationship, adoption rights, and so many things … We are really proud to be a part of this conversation,” he said.
The Indian government has opposed the appeals for same-s£x marriages, calling them “urban elitist views” and stating the parliament was the right place to debate the matter.
It has also said that such marriages are not “comparable with the Indian family unit concept of a husband, a wife and children”.
Mr Bhuptani said legalising same-s£x marriage faces “legal limitation” as it can only become a legislated law through parliament.
However, the ruling on Tuesday provided a hopeful message as the court asked the central government to form a “committee” to look into entitlements for same-s£x couples, he said.
“We are hoping that central government committee will have LGBT people, and I hope the committee will give a positive judgement.”
Mr Ghosh said he “fears the willingness of the parliamentarians” to recognise same-s£x marriage, but “the fights will still be going on”.
“We will be fighting for our rights. Equally, respect, dignity. That’s what we want,” Mr Ghosh said.
In 2012, the Indian government estimated there were 2.5 million LGBT people in India.
But LGBT rights activists say the figure could be as high as 135 million, which is about 10 per cent of the population.
Only Nepal and Taiwan allow same-s£x unions in Asia, where largely conservative values still dominate politics and society.