The 26 men, escorted by 80 German police officers, landed shortly after 7.30am in Kabul, airport police spokesman Mohammad Adjmal Fawzi told AFP.
He said at least one of the 26 was "suffering" and showing signs of psychological distress, adding: "He could be brought back to Germany."
Several of the refugees told AFP they had been arrested Monday morning at dawn and sent to Kabul with just a small piece of luggage or a backpack containing their belongings.
The men were the second batch of would-be refugees denied asylum by German authorities and deported, despite growing insecurity in Afghanistan.
The conflict caused some 9,000 deaths or injuries among civilians in the first nine months of 2016, according to the United Nations, which is to publish its annual report by the end of the month.
In 2015 the number of civilians killed or wounded was more than 11,000, the highest recorded since 2009, with children paying a particularly heavy price, according to UN figures.
Some 250 people staged a protest against the deportations at Frankfurt airport on Monday night, Sarmina Stuman of the Afghan Refugees Movement told AFP.
"Afghanistan is simply at war, which is why we are protesting against expulsions to a country like Afghanistan," she said.
In December, German interior minister Thomas de Maizière justified the expulsion of Afghans in order to preserve the "right" of asylum in the country, the only one in Europe to open its doors wide to refugees.
De Maiziere argued that Taliban attacks largely targeted "representatives of the international community" in Afghanistan and not the civilian population.
A first flight carrying 34 men arrived in Kabul in December, a third of whom were convicted of crimes ranging from theft to homicide, according to the German authorities.
That did not appear to be the case on Tuesday, when the passengers were able to leave the airport freely.
They will be sheltered by the government for at least two weeks after which they face an uncertain future, with Afghanistan already so overwhelmed by people fleeing fighting that officials have warned of a humanitarian crisis.