He was welcomed by two senior priests and a layman with the Russian traditional bread and salt at the entrance.
He was formally enthroned after senior bishops chanted "Axios!" - the Greek word for "worthy" - three times.
BBC religious affairs correspondent Christopher Landau says Kirill is a well-known face in Russia, having presented religious programmes on state television for some years.
Patriarch Kirill is seen by some as a moderniser, our correspondent says.
He certainly understands the potential of a high media profile.
But on social issues, like abortion and homosexuality, his words are resolutely conservative.
In addition to his TV show, Patriarch Kirill served as acting head of the Church after Alexiy II's death and has also been the head of the Church's external relations department for the past 20 years.
Warmer ties
That position has meant he has established relationships with other Christian leaders that may prove valuable in the years ahead
Kirill's appointment was welcomed by Russian Prime Minister Vladimir Putin and by the leader of the Roman Catholic Church, Pope Benedict XVI.
The two Churches split in 1054 and relations have been strained, with the Orthodox Church accusing the Vatican of trying to win Russian converts following the break-up of the Soviet Union.
But Kirill and the Pope have met each other several times, which could indicate a future warming of ties, says our correspondent.
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