The meeting in the small wood-paneled VIP room of Havana's airport was a landmark development in the 1000-year schism that has divided Christianity.
"We are brothers," the Pope said as he embraced Kirill. The men exchanged three kisses on the cheek.
"Now things are easier," Kirill agreed. "This is the will of God," the Pope said.
Later, the Pope flew into Mexico City's airport for a five-day visit during which he plans to bring a message of solidarity with the victims of drug violence, human trafficking and discrimination to that country's most violent and poverty-stricken regions.
The pontiff made no public remarks before making a 22km trip to the papal envoy's residence. Less than an hour after arriving, the Pope came out the gates to delighted screams from the faithful, accepted two white roses and prayed with those gathered.
In Havana, the two church leaders' meeting and signing of a joint declaration was decades in the making and cemented the Pope's reputation as a risk-taking statesman who values dialogue, bridge-building and rapprochement.
In the 30-point statement, the Pope and Patriarch declared themselves ready to take all necessary measures to overcome their historical differences, saying, "We are not competitors, but brothers."
The Pope and Kirill called for political leaders to act on the single most important issue of shared concern between the Catholic and Orthodox churches today: the plight of Christians in Iraq and Syria who are being killed and driven from their homes by the Islamic State group.