Isaf said a US soldier mistook the BBC Pashto service journalist for an insurgent when troops responded to a militant attack in the town of Tarin Kowt in southern Uruzgan province. Khpulwak was one of 19 people killed.
Nato launched an inquiry after initial reports that Khpulwak had been killed by insurgents were questioned.
The BBC said it recognised that Isaf had provided clarification, ending a period of uncertainty, but it would study the details of the findings on receiving the full report.
Director of BBC Global News Peter Horrocks said: “Ahmed Omed’s death further highlights the great dangers facing journalists who put their lives on the line to provide vital news from around the world. It is essential that journalists are given the best possible protection whilst reporting in dangerous situations so that the world can hear their stories.
“Our thoughts are with Ahmed Omed’s family and we will continue to do all we can to support them.”
Isaf’s findings concluded that Khpulwak, 25, was shot dead by an American soldier who mistook him for a suicide bomber.
Ahmed Omed Khpulwak sent text messages saying: “Death has come”
The report said that Isaf troops were responding to an insurgent attack on the offices of Radio Television Afghanistan.
The soldiers were attempting to clear the building after two suicide bombers had detonated devices when they noticed a man “with something clinched in one of his fists and reaching for something on his person with his other hand”.
The report said: “Based on the events of the preceding minutes the soldier assessed the actions as those of a suicide bomber who was taking steps to detonate an IED [improvised explosive device] that posed a lethal threat to numerous soldiers in the immediate area. He shot the individual with his M-4, killing him.”
The BBC’s David Loyn says Khpulwak had taken refuge in a bathroom and what he was holding up may have been his press card.
Isaf said Khpulwak’s death was tragic and has expressed condolences to his family.
Heavy fighting had broken out in Tarin Kowt’s market following three suicide bombings.
Heavy machine guns, rocket-propelled grenades and assault rifles were used by both sides, witnesses said. Afghan government forces received air support from Nato.
The Taliban admitted carrying out the attacks but denied killing the reporter, accusing government forces of shooting him as they fought to regain control of the area.
Khpulwak reportedly sent his brother two text messages at the time. The first read: “I am hiding. Death has come.” In the second, he wrote: “Pray for me if I die.”
US forces are renowned the world over for pulling the trigger first and checking ID later. However if a reporter is in a war zone then things like this can happen. Innocent people die in war zones.