Jefferson Lewis, 47, had to be airlifted to Darwin after an angry crowd attacked him then tried to storm an Alice Springs hospital, where he was taken following his arrest.
He is expected to be charged with the murder of the five-year-old girl, referred to as Kumanjayi Little Baby at her family's request and in line with cultural traditions.
An alcohol ban was slapped on Alice Springs on Friday after hundreds of people rioted outside the hospital in a bid to "get to Jefferson Lewis".
Tear gas was deployed, projectiles were thrown at officers and a police vehicle was torched.
Two officers, two paramedics and a firefighter were injured.
Senior Warlpiri elder and family spokesperson Robin Granites said he understood that people were angry but urged the community to let justice take its course.
"What has happened this week is not our way," he said in a statement.
"Our children are precious, of course we are feeling angry and hurt at what has happened.
"It is time now for sorry business, to show respect for our family and have space for grieving and remembering."
Lewis was found at a town camp about 10.30pm on Thursday, when he identified himself to people and was beaten by vigilantes.
He was unconscious when police arrived and emergency services were attacked when they tried to arrest him.
"The behaviour that we saw last night cannot be explained away, excused or accepted," Northern Territory Police Commissioner Martin Dole said.
"There is absolutely no excuse for violence against emergency services that are just doing their job."
Lewis was airlifted to Darwin in the early hours of Friday.
His injuries were not severe enough for him to be kept in hospital, police said.
He is expected to be charged in the coming days.
Mr Granites asked people in bush communities to carefully consider their need to travel to Alice Springs.
"If you need to come to join sorry business, that's fine. But just come for that, then return home please," he said.
"Now is not the time to be heroes on social media or make trouble."
Alice Springs community Elders also fronted the media in a bid to ease tensions after the community erupted in violence the same week it had banded together to search for the little girl.
"That hard work was undone last night by some people who were very angry with the system ... the same system that creates safety," Michael Liddle said.
NT Chief Minister Lia Finocchiaro said the community was angry and grieving, but there was "never an excuse" for a violent response.
The body of Kumanjayi Little Baby was found about noon on Thursday, five kilometres from the Old Timers Aboriginal Camp near Alice Springs where she was last seen.
It was the fifth day of a search which marked one of the NT's biggest investigations.
Alice Springs Mayor Asta Hill said the feeling in the community was "raw grief", urging people not to put others at risk.
Takeaway alcohol sales will be limited on Saturday as authorities attempt to stem further unrest.
The hunt has begun for rioters, with one woman arrested on Friday for attempting to torch a police vehicle.
Police were also looking for people they believed sheltered Lewis over recent days.
"My message to those people is, look out, because we're coming for you as well," Mr Dole said.
Prime Minister Anthony Albanese expressed condolences to the girl's family.
"It breaks your heart," he told reporters in Sydney.
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