During the incident the motorist got out of his vehicle and assaulted her, police said.
A Medical Examiner will conduct an autopsy to confirm the identity of the remains, but detectives believe the remains are those of the missing teen.
During the search, police also said an officer saw a vehicle driving erratically in the same area and stopped it, leading to the arrest of 22-year-old Martinez Torres as a suspect.
Police obtained a murder warrant that charges Torres for her death, the Fairfax County Police Department said.
Hassanen's mother told the Post that detectives said the girl had been struck with a metal bat.
The girl's father, Mohmoud Hassanen Aboras of Reston, said he doesn't understand how this could have happened, because he said his daughter, 17-year-old Nabra Hassanen, was a friend to everyone.
"I think it had to do with the way she was dressed and the fact that she's Muslim", Gazzar told the newspaper.
Virginia Lt. Gov. Ralph Northam sent his regards to the teen's family Sunday, adding that he and his wife were "deeply disturbed" by the assault and murder. Observant Muslims fast from sunrise to sunset during Ramadan, and since Ramadan this year overlaps with the summer solstice, and sunrise occurs well before 6 a.m., some Muslims will eat large meals in predawn hours.
Hassanen was the oldest of four siblings and was about to finish her sophomore year at South Lakes High School. The driver, identified as Torres, was arrested as a suspect in Hassanen's disappearance.
It is not being investigated as a hate crime, police say.
Police said Monday that the murder was not now being investigated as a hate crime.
The number of hate crimes in the US - and fatalities resulting from them - has skyrocketed since the election of President Donald Trump. She was wearing a traditional Muslim dress for women at the time of the incident.
"Pam and I are deeply disturbed by the assault and murder of a teenage girl in Fairfax last night", he said in the statement.
"We call on law enforcement to investigate and determine the motive of this crime and prosecute to the full extent of the law." the centre said in a statement.