Obama described himself as "incredibly moved" by his nearly hour-long session with the popular pontiff. He said the two spent the most time discussing the plight of the poor and the marginalized as well as regions of conflict and the elusive nature of peace around the world.
The Vatican, in a statement shortly after the meeting, said discussions centered on questions of particular relevance for the church in the U.S., "such as the exercise of the rights to religious freedom, life and conscientious objection" - issues that have fueled divisions between Obama and the church.
Contraception coverage and religious freedom have been central to the church's objections to Obama's health care law, which is facing a challenge on those grounds before the Supreme Court.
But Obama said those discussions took place with the Vatican Secretary of State Pietro Parolin, not with Francis. "We actually didn't talk a whole lot about social schisms in my conversations with His Holiness," he added. "In fact, that really was not a topic of conversation."
"I was grateful to have the opportunity to speak with him about the responsibilities that we all share to care for the least of these, the poor, the excluded," Obama said later during a news conference with Italian Prime Minister Matteo Renzi in Rome. "And I was extremely moved by his insights about the importance of us all having a moral perspective on world problems and not simply thinking in terms of our own narrow self-interests."
The marked difference in emphasis introduced a perplexing element to the long-anticipated meeting, which the White House has looked forward to as way to validate Obama's economic policies. In a report on Vatican Radio the day before the meeting, the Vatican had signaled that the divisive issues would indeed be on the agenda.
Obama emerged visibly energized from his audience with the pope, during which he invited Francis to visit the White House.
"It is a great honor. I'm a great admirer," Obama said after greeting the pope with a slight bow as they shook hands. "Thank you so much for receiving me."
Although Obama and the church remain deeply split over social issues, Obama considers the pontiff a kindred spirit on issues of inequality, and their private meeting in the Papal Library ran longer than scheduled. After they emerged to cameras, Francis presented Obama with a copy of his papal mission statement decrying a global economic system that excludes the poor. Obama said he would keep it at the White House.
"You know, I actually will probably read this when I'm in the Oval Office, when I am deeply frustrated and I am sure it will give me strength and will calm me down," Obama said.
"I hope," the pope responded.
Obama is the ninth president to make an official visit to the Vatican. His audience marked a change of pace for the president, who had devoted the past three days of a weeklong, four-country trip to securing European unity against Russia's aggressive posture toward Ukraine.
The president and pope both appeared tense at the start of the audience, when they initially greeted one another, but they were all smiles by the end of the meeting and seemed to have found a rapport, though they spoke through interpreters.
Later, Obama recalled the meeting as an elevated discussion about the role of empathy in public and private life.
"It's the lack of empathy that makes it very easy for us to plunge to wars," he said. "It's the lack of empathy that allows us to ignore the homeless on the streets."
But he also said that while he shared the pope's economic views, he didn't expect Francis to form a coalition or partnership with him on any issue.
"His job is a little more elevated," Obama said with a chuckle. "We're down on the ground, dealing with the often profane, and he's dealing with higher powers."
Obama arrived at the Vatican amid all the pomp and tradition of the Catholic Church, making his way in a long, slow procession through the hallways of the Apostolic Palace led by colorful Swiss Guards and accompanied by ceremonial attendants. The two greeted one another in the Small Throne Room, before sitting across from one another at the pope's desk, as is custom for a papal audience.
Obama presented the pope with a seed chest with fruit and vegetable seeds used in the White House garden, mentioning that he understands the pope is opening the gardens at the papal summer residence to the public. The chest was inscribed with the date of their meeting and custom-made of leather and reclaimed wood from the Baltimore Basilica - one of the oldest Catholic cathedrals in the U.S.
"If you have a chance to come to the White House, we can show you our garden as well," Obama said.
"Why not?" the pope responded in his native Spanish.
Although the Vatican has not yet confirmed the trip, it is likely that Francis will travel to the U.S. in September 2015 for the church's World Meeting of Families in Philadelphia. Popes have attended these family celebrations five of the past seven times they have been held, and Francis has put family issues at the forefront of his agenda.
House Speaker John Boehner, R-Ohio, has extended an invitation to the pope to address Congress when he visits the United States.
As Obama departed, he asked the pope, "Please pray for me and my family."
It was an echo of how Francis usually ends his meetings, asking for people to pray for him.