The girl was kidnapped in May by the same suspect who allegedly attacked her in December, according to a police report filed by her parents, a senior Delhi police official told CNN.
The suspect was reportedly out on bail while he awaited trial in the first rape case involving the girl.
Her parents told police the alleged attacker forced the girl to drink chemicals.
She died Sunday after being admitted to the hospital in June when she fell ill. The suspect was arrested again following her death, police said.
According to India's National Crime Records Bureau, more than four Dalit women are raped every day, with 2014 statistics saying crime against Dalits rose 19%. In many of the cases, these crimes are committed by perpetrators from an upper caste.
"For centuries, the lower caste (has) been subject to oppression, and one form of suppressing their empowerment has been through violence," Sunitha Krishnan, a rape survivor, activist and mental health specialist, told CNN.
"And to a woman or a child, the worst form of violence you can think of is sexual assault and sex crime."
Attacks on 4-year-old girl, Israeli woman reported
Unfortunately, such cases are by no means unusual, but the more sensational ones help increase visibility, according to Krishnan.
"We need to acknowledge that statistics say every 22 minutes a woman or a child gets raped in this country, and we need not only to break our silence but to act on it," she said.
"Sex crime is not only in India. You can single out India, saying that it is the only one having this problem, but it happens everywhere. However, in a country like India, these issues are not highlighted. For every 100,000 cases, only one gets highlighted."
Even in a country accustomed to stories of sexual violence, Sunday was particularly shocking.
That evening, a 4-year-old girl was allegedly raped by her 28-year-old neighbor in western Delhi, Rajendar Singh, inspector of Delhi police, told CNN. The girl is now in a stable condition.
In the northern Indian state of Himachal Pradesh, an Israeli woman, 25, was allegedly gang-raped by six men, Padam Chand, superintendent of Himachal Pradesh police, told CNN.
According to police, the woman said she was looking for a ride outside her guesthouse early Sunday when the driver of a car carrying the men offered her a lift to a nearby town.
In Delhi, such cases happen every two days, said Maliwal of the Delhi Commission for Women.
"It's become really sad, because we are concerned there is a lot of politics going on in Delhi, but we very strongly feel there is hardly any change being done on the ground," she said.