Zemarai said he was driving seven of his relatives home and was several hundreds metres away from the soldiers' vehicles when they opened fire.
"All of a sudden they opened fire at our vehicle.
his home before the burial of his son Zaryalai on Friday, he said:
"The first three bullets hit my car and the fourth one hit my 12-year old son in the side of his head."
The Afghan interior ministry said Nato troops had opened fire on a minivan "which apparently tried to overtake the troops or maybe the car was too close to the troops".
Zemarai has denied trying to overtake the convoy and said he was unaware of any warning shots.
Bays said he later counted four bullet holes in the bodywork of the damaged vehicle.
"The boy is the latest innocent victim of a Nato mistake and his father has said he would join the Taliban or any other group that would force foreign troops from his country," Bays said.
The area's police chief told Al Jazeera he was "deeply disturbed" by the incident involving International Security Assistance Force (Isaf) troops.
He said: "We've had this sort of problem all over Afghanistan.
"I hope the Afghan government deal with this seriously."
Bays said the police chief was later threatened with dismissal for speaking out over the killing.
A child was also hit and killed by a Nato vehicle in a convoy in the eastern province of Khost after he ran out from the side of the road, Isaf said in a statement late on Thursday.
Source: Al Jazeera and agencies