In the call, Mr. Netanyahu expressed regret for the raid, which took place as Israeli troops were enforcing a naval embargo on Gaza, and offered compensation, Turkish and Israeli officials said. The Turkish prime minister, Recep Tayyip Erdogan, accepted Israel’s gesture in the phone call.Afterward, officials from both countries said that diplomatic relations had been fully restored and that ambassadors would be reinstated.In a statement, Mr. Obama welcomed the call, saying, “The United States deeply values our relationships with both Turkey and Israel, and we attach great importance to the restoration of positive relations between them, in order to advance regional peace and security.” At one point, Mr. Obama, just before leaving for Jordan, got on the phone with both leaders as they spoke, one senior American official said.Israel and Turkey had cultivated close ties over many years, but the acrimony over the raid, which resulted in nine deaths, created a stubborn hurdle. Recently, Mr. Erdogan drew harsh criticism for saying that Zionism was a “crime against humanity.”Discussing the phone call, a senior Turkish government official said, “The Israeli prime minister, in a phone call that lasted 10 minutes, apologized to the Turkish nation for all operational mistakes, evident in an investigation, that led to human losses, and agreed to offer compensation.”Addressing the Gaza embargo that led to the tensions, a statement from Mr. Netanyahu’s office noted that Israel had also already removed a number of restrictions on the movement of people and goods to all the Palestinian territories, including Gaza, and that the openness would continue as long as quiet prevailed. The two leaders agreed to continue to work to improve the humanitarian situation in the Palestinian territories.On Friday evening, Mr. Obama landed in Jordan, where he is likely to confront pressure to help that financially struggling country cope with a desperate tide of refugees fleeing the civil war in Syria.It was Mr. Obama’s first visit to an Arab state since the Middle East erupted in unrest two years ago, toppling leaders in Egypt, Libya, Tunisia and Yemen, and plunging Syria, Jordan’s neighbor, into civil war. He held talks with King Abdullah of Jordan later on Friday.Diplomacy aside, Mr. Obama spent his last day in Israel and the West Bank making pilgrimages to symbols of the Holocaust, modern Zionism, the Middle East peace process and Christianity. In coming here, Mr. Obama traded symbolism for a still-unfolding crisis in Syria.About 3,000 refugees a day are fleeing into Jordan, swelling the ranks of Syrian refugees to 460,000, equivalent to 9 percent of the kingdom’s population. That has put a heavy strain on the Jordanian economy, a strain that is only partly offset by aid from the United States.Jordan is seeking increased aid from European and Persian Gulf states, which have lagged behind the United States in their support. Given a potential pool of three million or four million refugees in southern Syria, Jordanian officials fear that the daily influx could swell to as much as 50,000.Mr. Obama’s speech in Jerusalem, in which he appealed to younger Israelis to prod their leaders to pursue peace with the Palestinians, was warmly received in Jordan, where the king has been a steadfast, if somewhat despairing, advocate for the two-state solution.As he wrapped up his visit to Israel on Friday, Mr. Obama avoided politics for more universal themes.After rekindling the eternal flame and laying a wreath at the Yad Vashem Holocaust memorial in the morning, a solemn Mr. Obama spoke of a collective “obligation not just to bear witness but to act” against racism “and especially anti-Semitism.”“Our sons and daughters are not born to hate, they are taught to hate,” Mr. Obama said. “The state of Israel does not exist because of the Holocaust, but in the survival of a strong Jewish state of Israel the Holocaust will never happen again.”In the afternoon, he visited the Church of the Nativity in Bethlehem, the biblical birthplace of Jesus. A windstorm forced Mr. Obama to modify his travel plans to reach Bethlehem.With his helicopter grounded, he traveled by motorcade — a change welcomed by Palestinian officials, since it meant he would have to pass directly by Israel’s separation barrier.Outside the church, Mr. Obama, accompanied by the Palestinian president, Mahmoud Abbas, was welcomed by about 20 children in white shirts and dark pants, waving American and Palestinian flags.Mr. Obama also had lunch Friday with Mr. Netanyahu, a day after a speech that many analysts saw as harshly critical of Mr. Netanyahu’s handling of the peace process.Israeli newspapers were enthusiastic about the visit, saying the nation had fallen for Mr. Obama, but cautioning that his call for peace would not be easy to follow. Three newspapers used his declaration in Hebrew — “You are not alone” — as a front-page banner headline.“The most powerful man in the world arrived in the most threatened state in the world to promise love,” one columnist, Ari Shavit, wrote in the left-leaning Haaretz. “He gave us love every single second, in every speech and in every gesture.” But Mr. Shavit cautioned that “one cannot ignore the naïveté of Obama’s speech.”Palestinians, by contrast, were mostly disappointed. Some recoiled from Mr. Obama’s frequent use of Hebrew; his suggestion that he no longer sees a settlement freeze as crucial to restarting peace talks; and his repeated testimony to the United States’ eternal friendship with the nation they see as an enemy.“President Obama is eating, sleeping and chatting with people in Israel while he is spending few hours with Palestinian politicians,” said Said Kamal, a shopkeeper in Ramallah, the seat of the Palestinian Authority government in the West Bank, where Mr. Obama met Thursday with Mr. Abbas and Prime Minister Salam Fayyad.Mirvat Mohammad, 47, said, “America considers us as terrorists; therefore we will get nothing from this visit.” Mohammad Haj Yassin, an architect, said, “Since the last visit of the previous president, more land was confiscated; the U.S. administration did nothing about it.”Yousef Munayer, executive director of the Jerusalem Fund and Palestine Center, based in Washington, was one of several analysts critical of Mr. Obama’s speech as presenting “peace as a choice Israelis might make instead of an obligation they must fulfill.”On Friday morning, Mr. Obama was flanked, as he has been for much of the time since he landed in Israel on Wednesday, by Mr. Netanyahu and President Shimon Peres, who presented him with Israel’s Medal of Distinction at a state dinner Thursday night.At Yad Vashem, the group first visited the Hall of Names, a huge dome filled with photographs and dossiers describing the individuals who perished, then the Hall of Remembrance.Wearing a white skullcap, Mr. Obama arranged the wreath of red, white and purplish-blue flowers on a stone slab covering ashes of Holocaust victims, then stayed in a low crouch for a moment, head bowed. As a cantor sang the Jewish memorial prayer “El Mole Rachamim,” the president kept his head low and occasionally closed his eyes.“We can come here a thousand times and each time our hearts would break,” Mr. Obama said. “Here we see the depravity to which man can sink. We see how evil can, for a moment in time, triumph, when good people do nothing.”But he said that because the museum also told the story of rescuers, “this accounting of horror is a source of hope.”“We always have choices, to succumb to our worst instincts” and “to be indifferent to suffering,” Mr. Obama added, “or to display empathy that is at the core of our humanity.”