The deportations occurred a week after a deadly knife attack in the town of Solingen, of which the suspect is a Syrian citizen.
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Germany has deported Afghan nationals to their homeland for the first time since August 2021, when the Taliban returned to power.
Government spokesperson Steffen Hebestreit on Friday described the 28 Afghan nationals as "convicted criminals" but did not immediately respond to a request for comment to clarify their offences.
Interior Minister Nancy Faeser called the move a security issue for Germany.
Germany does not have diplomatic relations with the Taliban, requiring the government to work through other channels.
The deportations occurred a week after a deadly knife attack in the town of Solingen, the suspect of which is a Syrian citizen who had applied for asylum in Germany.
The suspected perpetrator was supposed to be deported to Bulgaria last year but reportedly disappeared for a time and avoided deportation.
He was ordered held Sunday on suspicion of murder and membership in a terrorist organisation pending further investigation and a possible indictment.
The Islamic State militant group claimed responsibility for last Friday's attack, without providing evidence.
The extremist group said on its news site that the attacker targeted Christians and that he carried out the assaults "to avenge Muslims in Palestine and everywhere". The claim couldn’t be independently verified.
There has also been debate over immigration ahead of regional elections Sunday in Germany's Saxony and Thuringia regions where anti-immigration parties such as the populist Alternative for Germany are expected to do well.
In June, Chancellor Olaf Scholz vowed that the country would start deporting criminals from Afghanistan and Syria again after a knife attack by an Afghan immigrant left one police officer dead and four more people injured.
On Thursday, Faeser announced a plan to tighten knife laws, according to German news agency dpa. Along with other officials in the governing coalition, she also pledged during a news conference to make deportations easier.