Jefferson Lewis, 47, is expected to be charged with the murder of a five-year-old girl, referred to as Kumanjayi Little Baby at her family's request and in line with cultural traditions.
He was flown to Darwin after an angry crowd attacked him, then tried to storm an Alice Springs hospital, where he was taken following his arrest on Thursday night.
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 as the situation escalated.
Two officers, two paramedics and a firefighter were injured.
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.
Alice Springs community Elders 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.
She said the town often made national news for the wrong reasons but was happy hundreds of people had earlier rallied to help find a girl they had never met.
"That's the Alice Springs that I know and that's who this town really is."
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 called for the community to unite in the aftermath of the violence as he expressed condolences to the girl's family.
"It breaks your heart," he told reporters in Sydney.
"We want to see the community come together, but we certainly understand people's anger and frustration and that was expressed."
Indigenous Australians Minister Malarndirri McCarthy told the ABC violence was not needed anywhere and police had to do their job as a family began the cultural grieving practice of "Sorry Business".
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