Wednesday's landmark decision, which coincided with International Day of the Girl Child, also raised the age of consent for all women to 18.
"In our opinion sexual intercourse with a girl below 18 years of age is rape regardless of whether she is married or not," read the ruling.
"The exception carved out in the Indian Penal Code (IPC) creates an unnecessary and artificial distinction between a married girl child and an unmarried girl child and has no rational nexus with any unclear objective sought to be achieved."
Jayna Kothari, who argued for Child Rights Group, an NGO that works to prevent child marriage, told CNN the ruling will create a "uniformity of laws".
"If you do not criminalize sexual intercourse within marriage with a girl that is under 18, you're implying that the Prohibition of Child Marriage Act (PCMA) is not worth enforcing. You're allowing marriages with girls that are minors but you're not doing anything about it."
Child marriage is illegal in India, but remains widespread throughout the country, especially in rural areas. According to a 2016 report by UNICEF, up to three million girls under the age of 18 are married in India every year.
Doing away with exceptions
Previously, there were discrepancies when it came to the ages specified in India's rape and child marriage laws.
Under section 375 of the IPC, intercourse with a girl below the age of 18 is considered rape, but a provision, known as Exception 2, did not punish a man for having sex his wife, even if he did not have her consent, provided she was above the age of 15.
Though marital rape is not a crime in India, the provision contradicted the age of consent in both the PCMA and the Protection of Children from Sexual Offences Act (POCSO).
The PCMA lists 18 as the age of marriage for girls and 21 for men. The age of consent is also 18 under POCSO.
India's underage brides
The Indian government had defended the controversial exception clause, stating that although the practice of child marriage is illegal, "the harsh reality is that 20 to 30 percent of female children below the age of 18 years got married in total violation of PCMA," according to the ruling.
The country's top court quashed that stance, describing sex with an underage wife as a "heinous crime which also violates the bodily integrity of a girl child, causes trauma and sometimes destroys her freedom of reproductive choice."
According to UNICEF, around one in four married Indian girls and women between the ages of 15-19 have suffered physical abuse at the hands of their husband.
As underage brides, many also become young mothers and suffer complications during pregnancy and childbirth.
"They are so young and because of that, they do not have the power or the authority to do anything. They cannot speak out against violence, they do not have the capacity to protect their own reproductive rights. This is part of their right to liberty and dignity," said Kothari.
A very toothless law
The reasons behind child marriage vary from region, caste and religion. In addition, the perception of daughters as a burden for poorer, lesser educated families often results in underage marriages.
But there are fewer taking place now. The percentage of women aged 20-24 who were married before 18 dropped from 47 percent in 2005/2006 to 27 per cent in 2015/2016, according to UNICEF.
The Supreme Court's reading down of Exception 2 and bringing it in line with the Constitution and other laws will force people to "wake up," according to Kothari, who is also the Executive Director of the Center for Law and Policy Research.
"Although the PCMA prohibits marriages under 18, it doesn't make those marriages invalid. You have to go to a court to invalidate them. It's a very toothless law but the criminal sanctions are strong. If you are now charged with rape, then you can actually go to prison. The numbers (of child marriages) will come down. It's not going to be overnight but it will seriously help the cause."