The law regards even consensual sex with a woman under 16 as rape, but an exception had been made for intercourse between a man and his wife who is between 15 and 18.
The move is being hailed by a step in the right direction for child rights and criminalisation of marital rape.
The Supreme Court had completed its hearing on the issue on September 6 and had reserved its judgment. The case came up through a writ petition filed by an NGO Independent Thought, questioning the constitutionality of a provision permitting a man to have physical relationship with his wife if she is aged between 15 and 18 years.
The court was, however, sceptical and asked the government if the exception was an incentive for child marriage. The top court further affirmed that the age of consent was 18 and will be not be lowered.
While expressing concern over the practice of child marriages in the country, the bench said social justice laws were not being implemented with the spirit with which they had been enacted by parliament.
India's 2011 census showed child marriage had declined marginally from a decade earlier but more than 5 million girls were still married before the legal age of 18.
The court also ruled that lowering the legal age for sex to 15, if the girl is married, would be illegal and unconstitutional, Srivastava said. The petitioner argued that under the law, a man is not considered guilty if he has sex with a child above 15.
"Therefore, simply because some marriages in India are being performed at an age lower than 18 years, it is not a justification to lower the age of consent to as low as 15 years".
According to Claudia Garcia Moreno, a leading expert in violence against women, "Child marriage marks an abrupt and often violent introduction to sexual relations".
In April 2016, the high-level Pam Rajput Committee strongly criticised the legislature for not criminalising marital rape as a whole. Its stand has been similar regarding marital rape, where it said that if recognised as a crime, it could "destabilize the institution of marriage, apart from being an easy tool for harassing husbands".