During the incident, which was caught on camera, lieutenant Caron Nazario, who is black and Latino, repeatedly asked what he had done wrong and said, "this is really messed up," as the officers holding guns demanded he get out of his car.
The police accused him of not cooperating.
Mr Nazario, wearing his military uniform, was driving a newly-bought SUV when the officers ordered him to pull over because he did not have permanent license plates, news reports said.
Virginia Governor Ralph Northam said in a statement earlier on Sunday he had instructed police to conduct an "independent investigation" into the incident, which he said was "disturbing and angered me."
Police in the United States have been hit with multiple allegations of racism and misconduct, including over the death of a black man in Minneapolis last year in a case that attracted international outrage.
A police officer is currently on trial over George Floyd's death, facing charges of manslaughter and murder.
The Washington Post said that Mr Nazario, a health administration officer with the Virginia National Guard, was driving home on 5 December when he was pulled over.
Footage from the officers' bodycams and Mr Nazario's phone spread rapidly over the weekend after Mr Nazario filed a lawsuit on 2 April seeking $1 million USD in damages.
He was released without charge after the incident.
The lawsuit reportedly claims police threatened to end his military career if he spoke out about the officers' conduct.
"We must keep working to ensure Virginians are safe during interactions with police, the enforcement of laws is fair and equitable, and people are held accountable," Mr Northam said.