Koang Wuordol, 22, was arrested in Victoria and extradited to the Northern Territory on Monday following a two-week police investigation.
He was charged with murder on his arrival.
Two others, Guandong Lual Gatl Guandong, 22, and a 17-year-old, who cannot be named for legal reasons, were initially charged with accessory to murder after the fact, but have now been upgraded to murder.
"These arrests and subsequent charges have been the result of an incredibly large investigation spanning over two-and-a-half weeks with detectives, specialist investigators and forensic experts working around the clock, without rest, to bring closure to the family," Detective Acting Superintendent Joe Carbone said on Thursday.
"A young man has tragically had his life callously taken from him and police remain committed to holding those responsible to account."
The pair were in police custody for 144 hours without a charge, with the NT being the only jurisdiction allowing police to hold suspects for more than 48 hours pre-charge.
The body of 19-year-old Yiel Gatluak was found by a driver on a road near Undoolya Station at midday on January 1.
NT Police Assistant Commissioner Travis Wurst said the victim and accused trio were known to each other but police were still investigating if weapons were used.
"The forensic pathologist has advised us that the cause of death relates to blunt force trauma," he told reporters in Darwin on Monday.
"There aren't any penetrative wounds on the deceased.
"All items that were seized from the crime scene are being examined."
NT Police also said it has found a video it was searching for depicting Mr Gatluak being assaulted.
Other graphic videos circulating in Alice Springs depicting "beheadings" and assaults from other countries were not relevant to this investigation and police requested people stop sending them to detectives.
Mr Wurst told reporters on Monday the video would be crucial to the investigation.
"(The video) will be a significant piece of evidence ... making sure the persons charged ... are brought to justice," he said.
Wuordol appeared in Alice Springs Local Court on Tuesday where his matter was adjourned until March 7.
Guandong and the 17-year-old were both refused bail and are set to reappear in court March 7 and February 29 respectively.
Investigations into the death are ongoing.
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