The Supreme Court also threw out appeals from the families of three Beria associates shot on the same day as Stalin's henchman.
Russia TV said many people viewed the court's ruling as a landmark.
Family members said Beria has been the victim of political persecution, but the court upheld an earlier ruling by the military prosecutor's office.
The Supreme Court also threw out appeals from the families of three Beria associates shot on the same day as Stalin's henchman.
However, it partly rehabilitated another three, ruling that the death sentence had been excessive in their case.
Memorial for victims
Russian NTV at the weekend broadcast a memorial service held near Moscow for all the victims of Soviet repression.
The requiem, conducted by the patriarch of Moscow and all Russia, Aleksiy II, took place at Butovo, where thousands of wrongfully convicted citizens were executed during the Stalin terror years.
Mass repression
Beria headed the Georgian Communist Party from 1931-1938 and was in charge of interior and state security agencies until his arrest in 1953.
Russia's Interfax news agency said: "He was personally involved in the organisation of massive repression, a permanent feature of Josef Stalin's regime."
Beria was arrested in June 1953, shortly after Stalin died. The Supreme Court of the USSR sentenced him to death in December 1953 on charges of high treason, espionage anti-Soviet plotting, terrorism and rape.
His case was reopened in 1998 when his relatives applied for retroactive rehabilitation for a man they said had himself been a victim of political persecution.
BBC Monitoring (http://www.monitor.bbc.co.uk), based in Caversham in southern England, selects and translates information from radio, television, press, news agencies and the Internet from 150 countries in more than 70 languages.