Chancellor Angela Merkel vowed to tackle hatred after an attack on an German synagogue in October in the eastern German city of Halle killed two people on the celebration of the Jewish holiday of Yom Kippur.
Monday's two suspects, aged 21 and 33, were “known to the police” and were arrested near the cemetery in western Geilenkirchen, the Aachen police said in a statement.
A witness alerted police after seeing two people in hoods and wearing dark outfits knock over tombstones and spray some with blue paint overnight.
The German government had promised at the end of November to introduce a law making it possible to increase penalties when a crime involved an anti-Semitic motive.
Germany has seen a rise in anti-Semitic acts. Last year, they increased by almost 20 percent compared to 2017, according to police statistics, with the neo-Nazi movement blamed for most of them.