The Russian Foreign Ministry said that it was making the move "due to the reciprocity principle" and ordered them to leave the country within the next seven days.
Germany expelled the Russian Embassy employees on Dec. 4 after Russian authorities didn't answer requests by Germany to help shed light on the daylight slaying of a Georgian man in Berlin on Aug. 23.
Russia expelling German diplomats in response "sends the wrong signal and is unjustified," the German Foreign Ministry said in a statement Thursday.
German federal prosecutors took over the investigation after concluding that evidence suggested involvement either by the Russian government or Chechnya.
Russian President Vladimir Putin this week alleged the slain man was "a bandit" and "a murderer" and said Russia repeatedly asked Germany to extradite him, but to no avail. German authorities say they weren't aware of any extradition requests for the victim from Russia.
"The man who died in Berlin took active part in fighting in the Caucasus. He was on a wanted list, he was a militant, a very cruel man who shed a lot of blood. He was responsible for the death of 98 people in just one attack. He was one of the organizers of explosions on the Moscow subway," Putin said.
Kremlin spokesman Dmitry Peskov said Thursday that the victim's alleged "participation in incredibly bloody terrorist acts and mass murders" in Russia had been established by the country's law enforcement agencies.