Embassy spokeswoman Caitlin Hayden said the bodies were being transported by U.S. military aircraft and accompanied by FBI personnel.
"In accordance with their families' wishes, the remains of two American citizens will remain in Afghanistan and be laid to rest here, in the country they selflessly and courageously served for so many years," she said.
Ten members of an International Assistance Mission medical team - six Americans, two Afghans, one German and a Briton - were ambushed and killed Aug. 5 by gunmen in Badakhshan province. The team set off from Afghanistan's capital, Kabul, for remote Nuristan province to operate a mobile clinic with eye doctors, a dentist and a general practitioner for people with little access to medical care.
Elsewhere, NATO reported that a U.S. service member died Wednesday following an insurgent attack in southern Afghanistan. The coalition did not disclose the location or details of his death.
NATO also reported that a roadside bomb killed three Afghan civilians and wounded three others Tuesday while they were driving in the Waghaz district of Ghazni province in eastern Afghanistan.
It was the latest in a growing number of civilian deaths caused by insurgent forces.
The number of Afghan civilians killed or injured in the war soared 31 percent in the first six months of the year, with Taliban bombings and assassinations largely responsible for the sharp rise, the United Nations said in a report released Tuesday.
It found the number of deaths and injuries caused by NATO and Afghan government forces dropped 30 percent compared with the first six months of last year, largely a result of curbs on the use of air power and heavy weapons.
But the overall sharp rise in deaths and injuries indicate the war is growing ever-more violent, undermining the coalition's aim of improving security for ordinary Afghans in the face of a virulent Taliban insurgency.
The U.S. command also reported that Taliban fighters fired four rocket-propelled grenades at a mosque near Asadabad in Kunar province on the first day of the Islamic holy month of Ramadan. One of the grenades hit the mosque, breaking windows and cutting down a tree but causing no casualties, it said.
Kunar Gov. Fazlullah Wahidi appealed for a halt in violence during Ramadan.
In the west, two suicide bombers died Wednesday inside a mosque when their explosive vests detonated accidentally, provincial police Chief Mohammad Faqir Askar said.
NATO also reported Wednesday that a joint Afghan and coalition force killed a senior Taliban commander, Maulvi Ghulam Haideri, and Maulvi Sher Agha, a Taliban operative, on Aug. 4 in the Sherzad district of Nangarhar province. Twelve other insurgents were killed in fighting, and 26 rocket-propelled grenades, multiple automatic weapons, grenades and about 1,000 rounds of ammunition were destroyed at the scene, it said.