Thousands of individuals and cargo vehicles crossed the border to enter the two countries through Torkham and Chaman border crossings, Geo TV reported.
Travellers, transporters and traders expressed happiness at the government decision.
“The two countries should resolve matters through discussions. Closing the borders is not the right way to find solutions,” a trader said.
Prime Minister Nawaz Sharif ordered on Monday that the Pakistan-Afghan border would reopen. The decision was a “goodwill gesture”, Sharif said.
It was reopened at 7AM on Tuesday, officials said.
The officials told Radio Pakistan that Afghans carrying valid documents alone would be allowed to enter.
Pakistan sealed the Torkham border crossing with Afghanistan for an indefinite period after the bombing at the Lal Shehbaz Qalandar shrine in Sindh province last month.
The border crossing was sealed for all trade and commercial activities due to security concerns.