Farid and Feriba Ahmadi, took refuge in the Ghausia Jamia mosque in Lye, Stourbridge, in West Midland last month when the home office ruled they had no case to stay in Britain on compassionate grounds.
The couple has two children who had been kept with some family friends for protection.
The raid was conducted by 12 police officers, some of them in riot gear and equipped with a battering ram.
The Afghan couple has been detained and preparations are being made to deport them to Germany where their asylum claim was being processed before they arrived in Britain.
There are fears that some Muslim groups may react to the manner of the arrests, and the storming of the mosque by the police, which can be viewed as desecration of a sacred place.