President Enrique Pena Nieto welcomed Francis at the airport while a mariachi band played before he climbed the popemobile to wave at crowds along the capital of the world's second largest Catholic country.
"Francis, brother of the Mexican people!" people chanted as thousands braved the evening cold, holding up telephones to light his way.
But before beginning a five-day trip that will take him across Mexico's violence-torn regions, Francis stopped in Cuba to mend a 1,000-year-old Christian rift with Russian Patriarch Kirill.
"Clearly, this meeting is God's will."
It was the first meeting between the heads of the Eastern and Western churches since the great schism of 1054 when the churches split apart, with the Eastern church rejecting the authority of Rome.
"For nearly one thousand years, Catholics and Orthodox have been deprived of communion in the Eucharist," they said in a joint declaration signed after they hugged and kissed at Havana's airport.
"Mindful of the permanence of many obstacles, it is our hope that our meeting may contribute to the re-establishment of this unity willed by God," the church leaders said.
Their meeting was driven by rising violence in recent years in the Middle East, where Christian communities have suffered violence at the hands of extremists.
"We call upon the international community to act urgently in order to prevent the further expulsion of Christians from the Middle East," they said.
Between them, they are the spiritual leaders of more than 1.3 billion Christians, but the Orthodox Church's refusal to accept the primacy of the Roman pontiff has been the main barrier to a rapprochement.
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