Alexy II's coffin was set on a raised platform covered in flowers at the centre of the cathedral. Two hundred Russian bishops and a choir joined in singing Russian Orthodox liturgy.
Russian President Dmitry Medvedev and Prime Minister Vladimir Putin were due to attend the service.
The patriarch died last Friday at the age of 79 after 18 years at the helm of the world’s largest Orthodox Church.
Following the service, Alexy II’s body will be taken to the Cathedral of the Epiphany for burial.
Over the last few days, thousands of mourners have filed past the patriarch’s open casket at Christ the Saviour to pay their last respects.
The Kremlin said that Russian President Medvedev had ordered all entertainment events and broadcasts to be cancelled throughout Tuesday.
Alexy II is credited with reconciling his Church with the Russian Orthodox Church Abroad and with reviving the domestic Church after years of repression under Soviet authorities.
He was unable to stifle the frequent accusations of opponents that he worked for the KGB and faced criticism for bringing the Church too close to the Kremlin.
Metropolitan Kirill of Smolensk and Kalingrad, a known reformer within the conservative Church, has been appointed interim leader until a new patriarch is chosen in the next six months.
