The US presidential aircraft landed at Queen Alia Airport near Amman at 1445 GMT, and Obama was welcomed by Jordanian Foreign Minister Nasser Judeh and other senior officials.
He headed to the royal palace for talks and a private dinner with King Abdullah II, a key US ally, on the agony of Syria's conflict in Jordan, which hosts more than 450,000 refugees from the war-torn country.
Obama will also support political reform efforts inside Jordan, which has been an oasis of relative calm in a region swept by turmoil of the Arab Spring.
The US leader wrapped up a three-day trip to Israel and the Palestinian territories, his first as president with a visit to Bethlehem's Church of the Nativity.
While the thrust of his Israel trip was reassurance Washington would mount an "eternal" defence of the Jewish state in the face of the Iranian nuclear threat, Obama is to focus on the Syria conflict on his overnight stop in Amman.
The number of Syrian refugees is expected to rise to 700,000 by the end of 2013, as people fleeing the vicious fighting between Bashar al-Assad's forces and rebels spill over its borders.
Obama has resisted pouring US arms or ammunition into the conflict, which the UN estimates has cost at least 70,000 lives, but has offered logistical support to rebels and hundreds of millions of dollars in humanitarian aid.
A senior US official said Obama wanted to coordinate with the king on security challenges and on helping Jordan alleviate the refugee crisis.
"We're also working very closely with the Jordanian government as part of the coalition of countries that is supporting the Syrian opposition to pressure the regime, to build up the opposition, and try to bring about a new Syria."
In Jerusalem, Obama said the United States was investigating claims chemical weapons had been used in Syria, warning it would be a "gamechanger" and that Assad's regime would he held accountable.
On Friday morning, Obama visited the grave of Theodor Herzl, the father of modern Zionism, then paid his respects at the grave of murdered Israeli premier Yitzhak Rabin, where he placed a stone from the grounds of Washington's Martin Luther King memorial.
He also toured Yad Vashem Holocaust Museum, saying it showed "the barbarism that unfolds when we begin to see our fellow human beings as somehow less than us".
After a brief meeting with Netanyahu, Obama set off for Bethlehem, travelling by motorcade, not helicopter, after a sudden sandstorm swept the city.
The change of plan gave Obama an unscheduled experience of the eight-metre-tall (26-foot) wall which loops around the West Bank city.
As the huge motorcade wound through the steep, narrow streets, crowds of onlookers watched in silence, with no sign of the enthusiasm which usually greets the convoy.
Some held up signs of protest reading: "No return no peace."
Inside the cavernous, dark interior of the church, he was briefly shown around by Palestinian president Mahmud Abbas.
In a powerful direct appeal to young Israelis on Thursday, Obama declared the two-state peace solution was very much alive and their only hope of true security, urging them to try and see the situation through Palestinian eyes.
"Put yourself in their shoes, look at the world through their eyes. It is not fair that a Palestinian child cannot grow up in a state of her own, and lives with the presence of a foreign army that controls the movements of her parents every single day," he said.
The two-state solution was the only way to ensure Israel remained a Jewish state in view of the changing demographics, he said.
Earlier, Obama's edgy news conference with Abbas in Ramallah reflected Palestinian disappointment with his failure to live up to first-term vows to help them secure their own state.
The atmosphere lacked the bonhomie of his bonding session with Netanyahu on Wednesday, as the two sought to prove their prickly relationship was a thing of the past.
Although Obama singled out Jewish settlements as a major obstacle to reviving talks, he did not call for a new freeze, although Abbas insisted a construction moratorium was a must if negotiations were to resume, his adviser said.
The Palestinians for the most part went largely empty-handed, although the finance ministry said $200 million in aid, which had been blocked for months by Congress, had been freed up in the weeks running up to the visit.
Meanwhile, Secretary of State John Kerry, who is travelling with Obama, is to return to Israel on Saturday evening "to review the results of the president's visit following his stops in Ramallah and Amman," the State Department said.