"I was profoundly saddened to hear the news," the pope said in a message to the Russian Church's Holy Synod.
Alexy II, who led the Russian Orthodox Church for 18 years, died at the age of 79 in his residency near the Russian capital on Friday morning.
The pope recalled the patriarch's efforts to restore the Russian church, whose role had been weakened by years of Soviet rule. He said Alexy II fought for "for human and Gospel values".
A senior church official said heart failure was believed to be the cause of death. The patriarch was known to have suffered from health problems in recent years.
Alexy II became patriarch of the Russian Orthodox Church in 1990, shortly before the collapse of the Soviet Union, and presided over a religious revival in Russia, with thousands of churches and monasteries being restored and hundreds of new ones built across the country.
Under his leadership, Russia's last tsar, Nicholas II, and his family shot by the Bolsheviks in 1918, were canonized as well as many New Martyrs who suffered under communism.
Alexy II openly objected to then Pope John Paul II's visit to Russia, accusing the Catholic Church of attempts to poach converts in Russia and neighboring Ukraine.
In 2007, he signed a reunification act with Metropolitan Laurus, head of the Russian Orthodox Church Outside of Russia (ROCOR), after almost 90 years of separation. The foreign branch broke away in 1921, after accusing fellow clergymen in Soviet Russia of collaboration with the country's communist regime.