The Afghan Foreign Ministry said the ambassador's daughter, Silsila Alikhil, was kidnapped on Friday evening while in her rented vehicle in Islamabad. She was tortured for several hours, and eventually released.
The Islamabad police has launched an investigation but no suspects have been arrested so far.
The Afghan ministry said it was in contact with the ambassador and his family and was extending full support in the matter.
According to a hospital medical report, Silsila suffered blows to her head, had rope marks on her wrists and legs and was badly beaten.
There is also suspicion that she had several broken bones, according to Afghan officials.
Security forces to use 'all resources' in hunt for suspects
Pakistani Prime Minister Imran Khan has directed the interior ministry to "utilize all resources to apprehend the persons involved" in the kidnapping.
Interior Minister Sheikh Rashid Ahmed said that the police and other law enforcement agencies have been asked to apprehend the culprits within 48 hours.
The Pakistan government said security at the residence of the Afghan ambassador in Islamabad has been reinforced.
The incident comes amid tensions between the two neighboring countries with Afghanistan claiming Pakistan is sending thousands of jihadi militants over the border and providing safe haven for the Taliban.
Pakistan in turn accuses Kabul of harboring anti-Pakistani groups.
A leading female senator in Pakistan, Sherry Rahman, condemned Friday's attack. She tweeted that "the Afghanistan Ambassador's daughter is a young woman, and should not face ANY obstacle in walking about in central Islamabad".