The government earlier had said it would consider each deportation on a case-by-case basis following Wednesday's deadly attack in Kabul, which raised fresh questions about security in the country.
The German embassy was badly damaged in the attack, which killed at least 90 people in the Afghan capital.
The partial suspension of deportations will continue until Germany's foreign ministry issues a revised security assessment for Afghanistan next month.
The foreign ministry said voluntary returns would continue, as would the deportation of convicted criminals, people deemed a "terrorist threat" and "rejected asylum- seekers who persistently refuse to reveal their identity." Germany canceled a plane that was to take deportees to Kabul following Wednesday's attack.
Tens of thousands of Afghans fleeing the conflict in their home country have sought asylum in Germany in recent years. Germany has granted asylum to almost 60 percent of Afghan applications, a rate that is significantly higher than in other European Union countries.