Qhamar Gul, 15, and brother Habibullah fought back with an AK-47 assault rifle when their home was attacked, Ghor province spokesman Arif Aber told CNN Wednesday.
The children's father, a tribal elder and government supporter, and their mother were killed by insurgents around 1 a.m. local time on July 16 in the Tyora district, Aber said.
Qhamar and Habibullah Gul are now "in a safe place," Aber said, without specifying the location.
The Taliban's aim is to impose its interpretation of Islamic law on Afghanistan and remove foreign influence from the country.
On February 29, the United States and the Taliban signed a historic agreement that sets in motion the potential for a full withdrawal of US troops from Afghanistan.
The "Agreement for Bringing Peace to Afghanistan" outlines a series of commitments from the US and the Taliban related to troop levels, counterterrorism and the intra-Afghan dialogue aimed at bringing about "a permanent and comprehensive ceasefire."
However, in the month following the signing of the deal the Taliban increased its attacks on America's Afghan allies to higher than usual levels, according to data provided to the Pentagon's Special Inspector General for Afghanistan Reconstruction.
Despite the continued attacks on Afghan National Defense and Security Forces, on July 14 the Pentagon announced the US has withdrawn from five bases in Afghanistan and reduced the size of its forces in the country.