Patriarch Kirill addressed the gathering outside the Christ the Savior Cathedral and said collective prayer would "multiply our spiritual strength" in the face of mounting attacks this year by non-believers.
Similar prayer rallies were held by bishops throughout Russia in a concerted effort to shore up faith, the report said.
In February, a punk band overtook the main altar of Moscow's main cathedral and performed a song with profanities against the church and Prime Minister Vladimir Putin. Since, vandals have desecrated churches and holy objects in Russian cities, the report said.
The church has also been targeted in some media for its opposition to same-sex marriages and consumerism, which the church's Supreme Council denounced in a statement earlier this month as coming from "those pushing through radical liberal values."