The Navy SEAL, whose name has been withheld, was part of a four-member reconnaissance team that went missing after being ambushed in the mountainous east of the country.
The area has been the scene of recent intense fighting,
Two other commandos were found dead on July 4, the day after the only surviving team member was rescued.
A special forces Chinook helicopter that was sent to find the commandos was shot down by militants, killing 16 troops.
According to the Agence France Presse (AFP) news service, Taliban spokesman Mullah Abdul Latif Hakimi earlier stated that Islamic militants had held the missing commando hostage and then beheaded him on July 9, leaving his body on a mountainside.
But this account was rejected by the US military.
“He died while fighting his pursuers on or about June 28 in Kunar (province),” spokesman Colonel James Yonts said in a weekly media briefing in Kabul.
Violence has been escalating in Afghanistan since March, with at least 33 US soldiers killed in action over the past four months.
That trend is expected to continue as the country prepares for parliamentary elections on September 18.
Colonel Yonts said the US would soon deploy an additional airborne battalion of 700 troops to bolster security.
There are currently 16,700 US personnel serving in a US-Led foreign force hunting down Islamic militants.
Australia’s contribution to Afghanistan is expected to be discussed by the federal cabinet in Canberra, amid increased pressure from the Labor opposition.
In 2001, Australia sent more than 1,000 troops to Afghanistan, but that commitment has been scaled back to just one mine clearance officer.
Treasurer Peter Costello said that there is money available to fund a mission to Afghanistan, and that a request for help has also been received by the foreign minister.
Meanwhile, the US has suffered an embarrassing blow with the escape of four prisoners described by a spokesman as “dangerous enemy combatants”.
The four were being held at the heavily guarded Bagram Air Base detention centre, north of Kabul, and are thought to be the first to successfully break out of the facility.
A Bagram district official identified the men as: Syrian Abdullah Hashimi, Kuwaiti Mahmoud Ahmand Mohammad, Saudi Mahmoud Alfatahni and Libyan Mohammad Hassan.