Accompanied by Israel's Prime Minister Benjamin Netanyahu and President Shimon Peres, Obama laid wreaths at the graves of Theodor Herzl, the founder of modern Zionism who died in 1904 before realising his dream of a Jewish homeland, and former Israel prime minister Yitzhak Rabin, who was assassinated in 1995.
He also toured the Yad Vashem Holocaust memorial, declaring after that the memorial illustrates the depravity to which man can sink but also serves as a reminder of the "righteous among the nations who refused to be bystanders".
Friday's stop at Herzl's grave, together with Thursday's visit to see the Dead Sea Scrolls, the ancient Hebrew texts, were symbolic stops for Obama that acknowledged that the rationale for Israel's existence rests with its historical ties to the region and with a vision that predated the Holocaust. Obama was criticised in Israel for his 2009 Cairo speech in which he gave only the example of the Holocaust as reason for justifying Israel's existence.
"Here on your ancient land, let it be said for all the world to hear," Obama said at Yad Vashem on Friday, in a clear response to that criticism. "The state of Israel does not exist because of the Holocaust, but with the survival of a strong Jewish state of Israel, such a holocaust will never happen again."
Later in the day, Obama was traveling to Jordan where he planned to meet with King Abdullah II. Among the topics is Jordan's struggle with the influx of a half-million refugees from the Syrian civil war. Abdullah has voiced fears that extremists and terrorists could create a regional base in Jordan.
Before leaving for Jordan, Obama had lunch with Netanyahu and then took his motorcade to Bethlehem in the West Bank to visit the Church of the Nativity.
Israel's separation barrier
Obama had been scheduled to take a helicopter to Bethlehem but had to change plans due to unusually high winds. The route gave Obama a clear look at Israel's separation barrier with the West Bank, which runs south of Jerusalem and is the subject of weekly protests by Palestinians.
About 300 Palestinians and international pilgrims gathered near the Nativity Church, awaiting Obama's arrival. But a knot of protesters along the route held up signs stating: "Gringo, return to your colony" and "US supports Israeli injustice".
At a nearby mosque, Mohammed Ayesh, a Muslim religious official in Bethlehem, issued a plea to Obama in a speech to worshippers: "America, where are your values? Where are the human rights? Isn't it time that you interfere to make it stop?"
Amid high security, Obama toured the church with Palestine's Authority President Mahmoud Abbas. They stopped at the Grotto of the Nativity, which is said to stand where Jesus Christ was born. About 20 children waving US and Palestinian flags greeted Obama in a courtyard outside the sanctuary. He posed for photographs with Abbas and Bethlehem's mayor, Vera Baboun.
Earlier in Jerusalem, Obama and his Israeli hosts arrived at the sombre Herzl grave site under cloudless skies. Obama approached Herzl's resting place alone and bowed his head in silence. He turned briefly to ask Netanyahu where to place a small stone in the Jewish custom, then laid the stone atop the grave.
"It is humbling and inspiring to visit and remember the visionary who began the remarkable establishment of the state of Israel," Obama wrote in the Mount Herzl guestbook. "May our two countries possess the same vision and will to secure peace and prosperity for future generations."
At Rabin's grave Obama was greeted by members of Rabin's family. He initially placed a stone on Rabin's wife's side of the grave, then returned to place one atop Rabin's side. In a gesture linking the US and Israel, the stone placed on Rabin's grave was from the grounds of the Martin Luther King memorial in Washington, the White House said.
Rabin, Obama told family members, was "a great man".
Chatting with the family, Obama joked that "Bibi arranged for perfect weather", using Netanyahu's familiar name. He then added that "Shimon plied me with wine" at the official state dinner on Thursday evening. At one point the talk turned to the singer who performed at the dinner, and Obama pointed out that he was known to sing, too. "They had me on YouTube," he said with a laugh. "Check it out – Obama singing Al Green."
At Yad Vashem, Obama donned a skull cap and was accompanied by Rabbi Israel Meir Lau, a survivor of the Buchenwald concentration camp who lost both parents in the Holocaust. Among his stops was Yad Vashem's Hall of Names, a circular chamber that contains original testimony documenting every Holocaust victim ever identified.
"Nothing could be more powerful," Obama said. – Sapa-AP