A senior Pakistani official said the US forces opened fire on Monday, mistaking a Pakistani patrol for al-Qaida or Taliban fighters.
"It was due to some misunderstanding," the official said, speaking on condition of anonymity.
Pakistan was the main supporter of Afghanistan's former Taliban regime until the 11 September 2001, attacks on the United States, when it chose to back US efforts to drive the Afghan rulers from power.
A statement from the Pakistani military's public relations department said a strong protest had been lodged with the US authorities about the incident.
It said US forces opened fire on the Pakistani patrol at 0500 GMT at a border post in the tribal Waziristan region, some 260 km southwest of the capital Islamabad.
The statement did not give any explanation for the shooting, the first such reported incident involving US troops operating in Afghanistan.
"It was due to some misunderstanding."
Pakistani forces and Afghan soldiers, assisted by a US-led coalition, patrol their own sides of the border which runs along a remote tribal belt where remnants of the ousted Afghan Taliban and al-Qaeda are believed to be hiding.
Pakistan and Afghanistan are trying to settle a row over the poorly defined 2,450 km border, with the United States mediating.
Relations between Kabul and Islamabad worsened in recent weeks with Afghan officials accusing Pakistani forces of intruding into Afghan territory, a charge strongly denied by Pakistan.
US and Afghan officials have also urged Pakistan to take steps to prevent remnants of the Taliban from crossing into Afghanistan for attacks on the US-led coalition forces and their Afghan allies.
Pakistan denies accusations of allowing the Taliban to regroup on its soil or cross into Afghanistan, and says it has arrested hundreds of the group's members and of al-Qaida, the main suspect in the 11 September attacks in the United States.