The crossing at Chaman in restive Balochistan province was closed after a clash killed 15 people on both sides in the first week of May.
"Pakistan has opened Friendship gate Chaman on humanitarian grounds in Ramazan on request from Afghan authorities," the army said in a statement.
It said that after the Chaman incident, Pakistan has its area under effective control after having pushed back Afghan Border police troops.
Army said census has been completed in the Pakistani side of the divided villages of Killi Luqman and Killi Jahangir.
It said no border violation will be acceptable and Pakistani troops will maintain their positions along International Border in Killi Luqman and Killi Jahangir.