Aljazeera's correspondent from Kandahar reported that the Pakistani soldiers were taken into custody after they attempted to sneak into Afghanistan's Spin Boldak area close to the border.
Pakistan is said to have deployed more troops on the border in response to the detentions.
The correspondent further said that Spin Boldak local residents had fled their homes, fearing a clash between the Afghan and Pakistani troops.
The latest face-off comes amid hightening border tensions between the two countries.
Matters had come to a head in July after Pakistan's embassy was ransacked in Kabul, amid shrill accusations of Pakistani intrusions into Afghanistan.
Pakistan reopened its mission following a temporary closure, only after Afghanistan's interim leader Hamid Karzai apologised and pledged not to allow any repeated attacks.
But tensions have not significantly eased along the Afghan-Pakistan border.
Pakistan backed the Taliban government for years until the 11 September attacks on the United States. Many Afghans harbour deep suspicion of their eastern neighbour till date.