The body of late President Sardar Mohammad Daud Khan was among dozens discovered at two mass graves in the Pul-e-Charkhi area, east of Kabul, six months ago, said Ahmad Farid Raaid, a spokesman for the Ministry of Health.
Daud Khan and 17 family members and associates were executed inside the presidential palace in Kabul during a communist-inspired coup in 1978, Raaid said.
Their bodies were taken to a secret location east of the capital and their whereabouts remained a mystery for nearly three decades until a former army general who was involved in the burial came forward earlier this year and identified the spot, Raaid said.
The killings ushered in an era of Soviet domination over the country that lasted for a decade.
Soviet troops rolled into Afghanistan in late December 1979. They occupied the country for 10 years and were forced to leave as the Soviet Union was collapsing in 1989.
Following the discovery of the mass graves in July, current President Hamid Karzai formed a commission to determine whether some of the remains were those of Daud Khan and his family.
Teeth molds were used to identify the late president's body but the key was a small golden Quran that was found with his remains, Raaid said.
"This Quran was given to him as a gift by the king of Saudi Arabia when he went on a trip" to the kingdom, Raaid said.