The 23-year-old man is accused of hitting the Aboriginal woman with his car on the Stuart Highway on Monday night in Darwin's outskirts.
Part of her leg was discovered on the busy roadway the following morning in the rural suburb of Coolalinga, 30km south of the city centre, triggering a massive police investigation.
The woman's body was later found concealed in bushland on Jenkins Road in Bees Creek, 15km south of the collision site, on Wednesday night after the man and a 50-year-old woman were arrested earlier in the day.
"Investigations are ongoing but at this stage we believe the body of the victim was removed from the scene by the driver and his accomplice after the collision," Detective Senior Sergeant Paul Morrissey said on Friday.
"To fatally strike someone with your vehicle and then go to great lengths to cover it up is reprehensible behaviour."
The man has been charged with hit and run, misconduct with regard to a corpse, attempt to pervert the course of justice, and destroying evidence.
The woman is accused of attempting to pervert the course of justice, destroying evidence and misconduct with regards to a corpse.
Police have not released details of the victim's identity or her age. A forensic pathologist who examined the partial leg on Tuesday determined she was either a teenager or an adult.
Det Snr Sgt Morrissey previously said her injuries were consistent with being struck by a vehicle.
A traveller driving on the four lane highway linking Darwin to Alice Springs and Adelaide spotted the partial leg on Tuesday morning.
Investigators were initially unsure if its owner was dead or alive, leading to a fruitless search of the NT's hospitals and medical clinics.
The man was arrested at a home in Palmerston near the accident site, while the woman was arrested at a property in the Darwin suburb of Winnellie.
Police allege the 50-year-old woman helped the man move the woman's body away from the highway in an attempt to conceal the crime.
The pair remain in custody and will appear in the NT Local Court in Darwin on Friday.
It was the 11th pedestrian fatality on NT roads in the past 18 months.
All were Indigenous and six involved hit and run incidents, according to NT police.
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