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JERUSALEM — Under persistent prodding from President Obama, Israel and Turkey resolved a bitter, three-year dispute Friday with a diplomatic thaw that will help a fragile region confront Syria’s civil war, while handing the president a solid accomplishment as he ended his Middle East visit.

The breakthrough took place in the most improbable of surroundings: a trailer parked on the tarmac of Ben-Gurion International Airport near Tel Aviv. Moments before Obama left for Jordan, Prime Minister Benjamin Netanyahu telephoned the Turkish prime minister, Recep Tayyip Erdogan, and apologized for deadly errors in Israel’s 2010 raid on a Turkish ship that was trying to bring aid to Palestinians in Gaza.

After years of angrily demanding an apology, Erdogan accepted Netanyahu’s gesture and both sides agreed to send envoys to each other’s nations, having recalled them in 2011.

Concerned about the deteriorating situation in Syria, the Obama administration had been anxious to mend relations between Turkey and Israel, two major regional powers on Syria’s borders.

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The president’s involvement, a senior U.S. official said, was crucial to both leaders, which is why Netanyahu scheduled the call before Obama left Israel. Erdogan insisted on speaking to Obama before the president handed the phone over to Netanyahu.

In the end, the call produced a win-win for all sides. Obama achieved reconciliation between two of the United States’ most important allies, while Turkey and Israel gained goodwill with the Obama administration, important for two nations that have made ties to the United States central to their foreign policies.

Turkey and Israel, along with Jordan, have also been three pillars of stability for the United States as it confronts a civil war in Syria that threatens to spill beyond its borders and destabilize the broader region.

“Both of us agreed the moment was ripe,” Obama said of Netanyahu at a news conference later in Amman, Jordan. He cautioned that the détente was a “work in progress,” and Turkey and Israel would continue to have significant disagreements as they mended fences.

Obama re-emphasized his support for Jordan, too, announcing after a meeting with King Abdullah that the United States would provide an additional $200 million in aid to help Jordan with the burden of caring for 460,000 Syrian refugees who have flooded the country.

Israel and Turkey have a variety of shared economic and security interests, and both are concerned about the unraveling situation in Syria. Turkey also could play a strategic role in Washington and Jerusalem’s efforts to stop Iran from developing a nuclear weapon, as well as in resolving the Israeli-Palestinian conflict.

It was the Palestinian issue that opened the rift between the two, when Israeli commandos raided a Turkish ship, the Mavi Marmara, as it was trying to break Israel’s blockade of Gaza to deliver supplies. Nine people were killed in clashes on board, prompting an international outcry, several investigations and a rebuke by the United Nations.

“The prime minister made it clear that the tragic results regarding the Mavi Marmara were unintentional and that Israel expresses regret over injuries and loss of life,” a statement issued by Netanyahu’s office said.

Obama also made three symbolic pilgrimages Friday: meeting with Christian leaders at the Church of the Nativity in Bethlehem; laying wreaths and stones at the graves of Theodor Herzl, the founder of modern Zionism, and Yitzhak Rabin, the slain prime minister and peacemaker; and visiting Yad Vashem, Israel’s Holocaust museum.

Material from The Washington Post is included in this report.

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