Patriarch Kirill, an ally of Russian President Vladimir Putin, led the sanctification ceremony in Trinity Cathedral which is part of a €100 million complex owned by the Russian government.
Anne Hidalgo, the Mayor of Paris and Svetlana Medvedev, wife of the Russian Prime Minister, attended the private ceremony.
At the service, Patriarch Kirill thanked France for granting permission for the complex to be built.
Putin had championed the building of the new Russian church in Paris but the project was heavily criticised by his opponents.
He was forced to play down suspicions that the new complex would be used to spy on government buildings and embassies in the area.
Putin was meant to visit the Paris church complex in October, but cancelled his trip amid French opposition at Russia's bombing of civilians in the Syrian city of Aleppo.