The two UN employees were recovered after a raid on a house in the east of the city after tracing mobile phone signals, senior police official Sultan Khawaja told PTI.
But there was no sign of the suspected abductors.
Sami Aslam and Farrukh Saleem went missing on Thursday night after they went to visit a water park in the Gulshan-e-Maymar area on the outskirts of Karachi.
The UNICEF (United Nations Children's Fund) also confirmed the recovery of its staff in a statement.
"The police led the investigation, in close contact with UNICEF and the staff members' families," it said.
The two officials belong to Hyderabad city and were on a visit to the water park.
In the past also, UN workers have been targeted by militant groups in anti-polio drives on the outskirts of the city which is plagued by ethnic, sectarian and militant violence.
Kidnapping for ransom is a major problem for the police in the city which is also the financial hub of Pakistan.
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