A 35-year-old Syrian identified as Abdalfatah H. A. is a suspected member of the Al-Nusra Front and accused of 36 counts of war crimes for participating in the mass killing of Syrian government employees in 2013, federal prosecutors said in a statement.
Spiegel reports that the man was arrested in Düsseldorf.
The other Syrian Abdulrahman A. A., aged 26, is allegedly a member of the same jihadist outfit and accused of managing one of its combat unit's funds, vehicles and weapons.
The men were detained by police from the western states of Baden-Wuerttemberg and North Rhine-Westphalia who also searched their apartments.
Separately, the southern state of Bavaria announced the arrest of a 33-year-old Bosnian who is believed to have supplied the Sunni militia Junud al-Sham with several vehicles.
German federal prosecutors have launched around a dozen investigations concerning alleged war crimes committed in Syria or Iraq, alongside dozens of cases of suspected membership of jihadist groups.
The investigations have gained momentum following the arrival of over a million asylum seekers since 2015, including hundreds of thousands of people from Syria and Iraq.
Last July, in the first such conviction in Germany, a German jihadist was sentenced to two years in prison on war crimes charges after posing for pictures in Syria with the severed and impaled heads of two government troops.