The two men were in a stationery shop at a market when they were picked up by the sleuths of country's premier intelligence agency National Directorate of Security (NDS) and taken to one of their detention centres along with the embassy's official vehicle.
The staffers were identified as Hassan Khanzada, visa assistant at the embassy, and Syed Munir Shah, staff driver, the 'Dawn' reported.
Khanzada was manhandled during the detention, it said, quoting a source.
The embassy approached the Afghan foreign ministry and sought immediate release of the two staffers.
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The Afghan foreign ministry, reportedly after a bit of dilly-dallying, conceded that the two had been taken into custody by the NDS, the report said.
Khanzada and Shah were finally released after three hours, it said, adding that it was unclear why the staffers were detained.
The incident serves another blow to the already fraught ties between the two countries.
It happened amid latest efforts by the US-led coalition in Afghanistan to mend fences between Pakistan and Afghanistan.