The busy border crossing in the north-west was closed on Sunday night due to clashes between the two sides which killed a Pakistan army Major and an Afghan border guard.
A security official said that the two sides held talks on the issue and agreed that border should be re-opened.
"It will not affect the ongoing construction of the gate which is important to regulate illegal border crossings," he said.
Pakistan also lifted curfew in the areas near the border which was imposed after gun battles with Afghans. Pakistan has already announced that no one will be allowed to enter through Torkham without valid documents from June 1.
After reopening of the border, only those carrying visa and entry permits would be allowed to enter. Pakistan has also announced that security gates will be constructed at eight recognised entry points from Afghanistan and patrolling of about 2,400-km long border will be increased to check illegal crossings.