Prime Minister Manmohan Singh led appeals for calm and police sealed off large parts of downtown Delhi, in the wake of an outpouring of anger that followed the December 16 assault.
The demonstrations passed peacefully, however, as mourners vowed the 23-year-old medical student's killing would serve as a tipping point for how the nation deals with violence against women.
The victim's gold-coloured coffin was prepared in a funeral parlour in Singapore, ready to be flown back to India, accompanied by her parents who were at her bedside when she was pronounced dead at Singapore's Mount Elizabeth Hospital before dawn.
Draped in a white flag, it was finally driven out of the Hindu Casket funeral home shortly before 9pm and was believed headed for the airport.
Protestors who gathered in the Jantar Mantar thoroughfare in central Delhi, scene of the largest protest, said the unnamed student's death was a wake-up call for a country in denial about the levels of violence that women face.
Bela Rana, who was among more than a thousand protestors in Jantar Mantar, said the outrage after the attack represented a sea change and that women were no longer prepared to suffer in silence.
"We are aware that this is not the first case, nor will it be the last case of gang-rape in India, but it is clear that we will not tolerate sex crimes anymore," said Rana, a Delhi-based lawyer.
After previous protests had been broken up by riot police, Saturday's passed off peacefully.
However when the chief minister of New Delhi, Sheila Dikshit, tried to join the crowds she was roundly heckled and quickly withdrew.
Some of the protesters, who also gathered in outlying areas of the capital, carried banners that read "Hang the Rapist", accompanied by a picture of a noose.
While the six men who had already been arrested have yet to be formally charged, they are now the subject of a murder investigation.
"We have booked all the six accused under section 302 of the Indian Penal Code. It is a non-bailable offence which carries the death sentence," police spokesman Rajan Bhagat told news agency.
Dharmendra Kumar, one of Delhi's most senior police officers, said formal charges were expected to be filed by January 3.
The police have been heavily criticized for their hardline tactics in trying to quash the protests, including the frequent use of teargas and water cannon.
Gang-rapes are a daily occurrence in India and many go unreported by victims who have little faith in an often painfully slow justice system and are deterred by the response they can receive from male police officers.
But the particularly savage nature of the attack in Delhi has brought simmering anger to a boiling point and prompted the government to promise better security for women and harsher sentences for sex crimes.
After boarding a bus on December 16, the student was attacked by the men who took turns raping her and assaulted her with an iron bar before throwing her and her male companion off the moving vehicle.
"We have already seen the emotions and energies this incident has generated," said Singh.
"These are perfectly understandable reactions from a young India and an India that genuinely desires change."
His comments were echoed by Sonia Gandhi.
"As a woman and mother, I understand the pain. Her fight will not go in vain," said Gandhi.
After the death was announced in Singapore, the Indian high commissioner TCA Raghavan spoke of the ordeal endured by the family of the victim, who hail from a rural Uttar Pradesh.
"They have repeatedly asked me to say how inspired they are by the many messages of support and condolences they have received," he said.
"This reinforces their view that the death of their child will lead to a better future for all women in India and in Delhi."