RNA - Police said they had carried out the raids on 19 sites after indications of a "possible concrete impending terrorist attack" by terrorists.
The men arrested were a 27-year-old Algerian and a 23-year-old Nigerian, Reuters reported.
Salafism is an ultra-fundamentalist ideology that is particularly prevalent in Saudi Arabia. It is intolerant of what its adherents consider "deviant".
The ideology is led by prominent Salafist preacher Ibrahim Abou-Nagie, who was born in a refugee camp in Gaza and moved to Germany when he was 18. He later became a German national.
Germany has banned several terrorist associations in recent years, including Daesh in 2014.