On his way out of Israel, the president sat in on a phone call between Israeli Prime Minister Binyamin Netanyahu and his Turkish counterpart, Recep Tayyip Erdogan. Netanyahu, talking from a trailer at the airport, apologized to Erdogan for the deaths of Turkish nationals in a confrontation in 2010 between the Israeli military and a Gaza relief flotilla.
Jordanian King Abdullah II and his son, Crown Prince Hussein bin Abdullah, greeted Obama on his arrival at al-Hummar Palace in Amman. Obama shook hands with the king and prince and was overheard explaining he arrived an hour late because of a dust storm.
In addition to his visit to the Holocaust memorial, Obama visited the graves of Theodore Herzl, founder of the Zionist movement, and Yitzhak Rabin, the prime minister who was assassinated in 1995 after signing the Oslo Accords with Palestinian leader Yasser Arafat, The Washington Post reported. Obama laid stones on both graves.
He also visited Bethlehem, the birthplace of Jesus Christ.
At Yad Vashem, Obama said Friday bigotry and hatred have no place in a civilized world.
"Nothing equals the wrenching power of this sacred place ... ," Obama said. "We could come here a thousand times, and each time our hearts would break."
The memorial is a reminder that people are faced with the choice to "succumb to our worst instincts or to summon the better angels of our nature," Obama said.
"For us, in our time, this means confronting bigotry and hatred in all of its forms, racism, especially anti-Semitism. None of that has a place in the civilized world -- not in the classrooms of children; not in the corridors of power. And let us never forget the link between the two. For our sons and daughters are not born to hate, they are taught to hate. So let us fill their young hearts with the same understanding and compassion that we hope others have for them," Obama said.
Obama's three-day trip to Israel was his first visit to the country as president.
Jordan, a country of 6.5 million people, has taken in more than 360,000 refugees fleeing the Syrian civil war -- with the number expected to rise to 1 million by the end of the year, U.N. High Commissioner for Refugees Antonio Guterres said this month.
Syrian refugees enter Jordan at an average 1,200 people daily, officials say, but nearly 2,000 crossed the border into the country Tuesday and more than 1,700 more entered Wednesday, the official Petra News Agency reported Thursday.
More than 100,000 refugees are living in the overcrowded desert Zaatari camp, which was opened near the Jordan-Syria border last July and where security and crime problems are growing, Jordanian officials say.
Jordan's al-Ghad newspaper noted Friday while Obama and Abdullah were expected to discuss the refugee crisis, Obama had no plans to visit any refugee camps, which are straining the nation's resources.
Jordan is seen by U.S. officials as possibly playing a role in Middle East peace efforts because of its normalized relations with Israel. Abdullah's father, King Hussein, signed a peace treaty with Israeli Prime Minister Yitzhak Rabin in 1994.
Hussein was later honored when his picture appeared on an Israeli postage stamp in recognition of the good relations he established with Israel.
Obama spoke with Palestinian leaders and young Israelis about the peace process Thursday.
He urged Palestinians to return to the bargaining table even if Israel did not meet their condition of halting Jewish-settlement construction in Palestinian territories.
"If we're going to succeed, part of what we're going to have to do is to get out of some of the formulas and habits that have blocked progress for so long," Obama said in a joint news conference with Palestinian President Mahmoud Abbas after the two leaders met.
"Both sides are going to have to think anew," Obama said. "Those of us in the United States are going to have to think anew. But I'm confident that we can arrive at our destination to advance the vision of two nations, two neighbors at peace -- Israel and Palestine."
Abbas said it was "the duty of the Israeli government to at least halt the activity so that we can speak of issues. And when we define our borders and their borders together, each side will know its territory in which it can do whatever it pleases."
Abbas did not explicitly cite halting Israeli settlements as a precondition for entering into face-to-face talks with Netanyahu.
Those talks have been dormant since 2010.
Obama later told young Israelis they should empathize with their Palestinian neighbors living under occupation.
"Put yourself in their shoes," Obama said. "Look at the world through their eyes. It is not fair that a Palestinian child cannot grow up in a state of their own; living their entire lives with the presence of a foreign army that controls the movements, not just of those young people but their parents, their grandparents, every single day.
"It's not just when settler violence against Palestinians goes unpunished," he said. "It's not right to prevent Palestinians from farming their lands; or restricting a student's ability to move around the West Bank; or displace Palestinian families from their homes.
"Neither occupation nor expulsion is the answer," Obama said, "Just as Israelis built a state in their homeland, Palestinians have a right to be a free people in their own land."