But Vatican officials also raised social issues, including the birth-control mandate in ObamaCare and abortion, the Vatican said.
He downplayed the Catholic Church's concerns over the provision of the Affordable Care Act that requires employers to provide different forms of birth control as part of their insurance plans.
"We actually didn't talk a lot about social schisms," Obama said.
He said Francis "did not touch in detail on the Affordable Care Act," although he said the issue came up during a meeting with Secretary of State Cardinal Pietro Parolin. Catholic hospitals and universities have argued the mandate infringes on religious freedom, and some have sued the administration over the law.
Obama also said gay marriage and LGBT rights — two other areas where the president is on the opposite side of the church — "wasn't a topic of conversation."
In a statement describing the meeting as "cordial," the Vatican said the president and pope "discussed questions of particular relevance for the Church, such as the exercise of the rights to religious freedom, life and conscientious objection, as well as the issue of immigration reform."
The president said the leaders discussed how to help "the poor, the marginalized, those without opportunity." He said that while politicians had the task of developing policy solutions to address inequality, "His Holiness has the capacity to open people's eyes."
And, Obama said, the pair spent "a lot of time talking about the challenges of conflict and how elusive peace is around the world."
There was a specific focus on the Israel-Palestine peace talks, the civil war in Syria and the persecution of Christians in Lebanon.
The Vatican said both leaders expressed hope that in areas of conflict, "there would be respect for humanitarian and international law and a negotiated solution between the parties involved."
The meeting with the pope came less than 24 hours after Obama called on European allies to increase economic and diplomatic pressure on Russia over its military annexation of Crimea.
The pair also spent substantial time discussing immigration reform efforts in the United States.
"As someone who came from Latin America, I think he was very mindful of the plight of so many immigrants who are wonderful people working hard ... and yet they still live in the shadows," Obama said.
The pair also "stated their common commitment to the eradication of human trafficking throughout the world," the Vatican said.
Still, Obama downplayed the notion of a "partnership" between the pope and politicians such as himself.
"We deal with the often profane and he's dealing with higher powers," Obama said.
If the conflicts over the contraception mandate or abortion rights soured the discussion, neither leader showed it when exchanging gifts after their meeting.
The pope offered President Obama two medallions and a copy of the Joy of The Gospel, his apostolic exhortation critical of trickle-down capitalism, joking it was "for when you are bored."
The president has cited the pope's comments when arguing for his own domestic economic agenda to address income inequality, and the gift appeared a symbolic endorsement of that appropriation.
"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 said.
Obama's gift also served as a symbolic nod to the pope's efforts to broaden the church's outreach and charity. He presented Francis with a seed chest containing fruit and vegetable seeds from the White House garden, noting that the pope had announced earlier this year he would open the gardens of his summer residence to the public.
Obama also asked a favor of the pontiff as he departed. "My family has to be with me on this journey. They've been very strong. Pray for them. I would appreciate it," the president said.
The president said he was "extremely moved" by the pope's "insights of us all having a moral perspective on world problems, and not thinking only in terms of our own self interest."
He said the meeting was a "great honor" and that he was "incredibly moved by his compassion, his message of inclusion."
— This story was last updated at 2:03 p.m.