Alexiy, who forged close ties with the Kremlin under former President Vladimir Putin and helped revive the Church after the collapse of the Soviet Union, died on Friday at his residence outside Moscow. He died of heart failure after a long illness.
At Orthodox church services across Russia's 11 time zones, people said prayers through the night for Alexiy, who helped heal an 80-year rift with a rival faction set up abroad by monarchists fleeing the atheist Bolsheviks.
A Holy Synod will meet on Saturday to elect an interim Patriarch, known as the Patriarchal Locum Tenens. A wider synod will then convene to elect a new leader within six months.
"A session of the Holy Synod of the Russian Orthodox Church will take place on December 6 to elect Patriarchal Locum Tenens who will chair the Memorial Commission," a spokesman for the Moscow Patriarchy said.
Alexiy will be laid in state on Saturday in the giant Christ the Saviour Cathedral in central Moscow, rebuilt during Alexiy's reign after its destruction under Stalin. His funeral will take place on Tuesday, the Patriarchy said.
Believers laid hundreds of red and white roses at the Patriarch's office in central Moscow, a Reuters reporter said. White roses were said to be Alexiy's favorite.
Alexiy, who criticized the Catholic Church for trying to steal converts, is credited by many Russians for helping to revive Orthodoxy and boost church attendance in the moral and spiritual vacuum created the collapse of the Soviet empire.
Despite Soviet-era suppression of believers -- and the destruction of hundreds of churches under Stalin -- Orthodoxy remains a key part of life for millions of Russians.
Alexiy also steered a careful path for the Orthodox Church, which was riddled with divisions, especially during the upheavals of the 1990s.
"Alexiy's main achievement was to keep the Church together in this period of growth and turmoil," Andrei Zolotov, an expert on the Russian Orthodox Church, said by telephone from the United States.
"The Patriarch steered a very careful centrist path in the development of the church when it was threatened with being literally being torn apart politically, theologically and in many other regards too," Zolotov said.
Putin and President Dmitry Medvedev, who both attended major Orthodox Ceremonies with Alexiy, praised the Patriarch's role in helping form Russian statehood and for uniting the nation.