Wearing pink and some dressed in T-shirts bearing the face of Kumanjayi Little Baby, the crowd gathered under grey skies in the Red Centre capital on Saturday.
Family members surrounded a small coffin adorned with flowers and cried together.
Grandfather of Little Baby, Robin Japanangka Granites, opened the funeral to the public to allow the community to grieve as one.
"You come because you are one of our family," he told them.
"You are from here and we need you because we both cried at that same time."
In a eulogy read on her behalf, Little Baby's mother Jacinta Roy urged her daughter be remembered for who she was, not just her death.
She loved watching Masha and the Bear and Bluey, as well as playing games on her mum's phone, Ms Roy remembered.
The young girl also loved cuddling puppies and the colour pink.
"As a mother, my heart breaks into a million pieces," she said.
"I miss her.
"As a Christian, I would like to thank Father, Son and Holy Spirit for gifting me with a beautiful, precious little baby girl for the precious time that I was her mother here on Earth."
The family of the allegedly murdered girl invited the desert community to farewell her on Saturday while embracing her favourite colour.
The service comes months after her disappearance sparked one of the largest searches in Northern Territory history.
Kumanjayi Little Baby - so named for cultural reasons following her death - went missing from Old Timers camp on the outskirts of Alice Springs in late April.
It prompted an intensive five-day search by emergency services and local volunteers in grassy bushland.
The discovery of her body prompted a nationwide outpouring of grief, with vigils held across the country.
The arrest of 47-year-old Jefferson Lewis over her death sparked a riot outside Alice Springs Hospital, where angry locals demanded he be handed over to face traditional justice.
Lewis was flown out to Darwin, where he awaits his murder trial.
Mr Japanangka Granites, a Warlpiri Elder, thanked locals for their efforts to locate her and for their support of his family.
Kumanjayi Little Baby would be with our "father in heaven", he said at the time.
Sweeping changes have been recommended for the NT's child protection system after a review found workers repeatedly failed to adequately assess safety threats to Kumanjayi Little Baby's family.
The independent review, led by former NSW police commissioner Karen Webb and senior public servant Greg Shanahan, was tabled in the NT parliament in July.
Despite repeated indicators of domestic and family violence, the implications for the child's safety were not adequately recognised and protective responses were not pursued in a timely manner, the report said.
It found a domestic and family violence risk assessment was never done and as a result, an ongoing pattern of violence in the child's life and family environment was not fully recognised.
Operational delays were driven by high workloads and capacity issues, including retention and recruitment challenges in remote areas, the report said.
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