The church did not reveal the cause of death, although Alexy II, who died at home, had a history of heart problems, The New York Times reported.
The Holy Synod, the church's ruling body, is expected to meet in an emergency session Saturday, RIA Novosti, the Russian news agency, reported.
Alexy II was named patriarch in 1990, just before the breakup of the Soviet Union, the Times reported. He deepened the role of the church in everyday life, erecting and renovating cathedrals, introducing Orthodox education in public schools and becoming a prominent voice on moral issues.
The patriarch also lobbied the government to adopt restrictions on other Christian denominations to hinder their efforts to attract followers in Russia.
Relations between Alexy II and the Roman Catholic Church were tense during the patriarch's tenure over the issue of proselytizing. Because of this fissure, he would not agree to a visit to Russia by Pope John Paul II.