The Russian Orthodox Church still follows the Julian calendar, meaning that Christmas Day falls on January 7, a public holiday in Russia, instead of December 25.
In a televised Christmas message to Russians, Patriarch Kirill, head of the Russian Orthodox Church, called on followers to preserve their faith "to ensure a progressive development of history, to prevent ruptures, disintegration and breaches of the historic fabric."
Putin visited a convent outside the Black Sea resort of Sochi, lighting a candle bare-headed and in an open-collared shirt along with parishioners in the icon-lined church.
He did not appear with his wife Lyudmila, who is a devout Orthodox believer, but is rarely seen in public with her husband.
Prime Minister Dmitry Medvedev and his wife Svetlana attended the main Christmas service led by Patriarch Kirill in Moscow's central cathedral of Christ the Saviour, along with more than 5,000 worshippers.
Russia's leaders have made a habit of attending Orthodox services since Boris Yeltsin attended a Christmas service in 1992, making a break with Soviet authorities' espousal of atheism.
In a Christmas message published on the Kremlin website, Putin said that Russians were unified by "traditional spiritual and moral values that play a special role in Russian history and serve as a support to our society".
He praised the Russian Orthodox Church and other Christian confessions for "cooperating more closely with state and public organisations" in areas such as education and support for the family.
More than three million Russians attended services across the country in more than 9,000 churches, the interior ministry responsible for crowd control estimated.
The Russian Orthodox Church has been rocked over the last year by the case of balaclava-clad punk group Pussy Riot, which performed a "Punk Prayer" in Moscow's cathedral of Christ the Saviour, criticising Putin's close ties with the Church.
The Church used the case to rally believers, arguing that it is under threat from malign secular forces.
But the women's jailing has divided the public, with some feeling that the influential Church should have called for leniency towards the women, two of whom are now serving two-year sentences in prison camps.