As signs of the potential difficulty ahead, Obama pointed to "tensions and issues there that have to be resolved," but he said U.S. and Israeli officials were working on them and praised steps by Israel this week to ease its land blockade of Gaza.
Netanyahu's visit this week was first and foremost about fence-mending, in full view of the watching world. As part of that, Obama said he was committed to Israel's security and pledged to "back that up, not just with words but with actions."
Netanyahu, reciprocating, praised the "depth and richness" of U.S.-Israeli ties, invoking the American writer Mark Twain by name in saying that the "reports of the demise of the special relationship ... are just flat wrong."
The warm words distinguished the visit from Netanyahu's last call in March, when he was consigned with his aides to a White House work room while Obama dined with his family. The mood was so chilly on that visit that television cameras weren't even allowed up close to witness the men's personal interaction.
A few weeks before that clash, Israeli officials had humiliated the White House by approving new Jewish housing development in a disputed area of East Jerusalem precisely when Vice President Biden was traveling in Israel. Biden's trip had been seen as a precursor to a possible visit by Obama, but talk of that prospect ceased immediately.
In recent days, the Netanyahu government was sending different signals. In a weekend cabinet meeting, Netanyahu publicly set direct talks with Palestinians as a top priority for his conversation Tuesday with Obama.
To smooth the way, Israeli officials Monday announced new terms of their plans to ease the blockade on delivery of supplies to the Gaza Strip.
Then, on Tuesday, the Israeli military announced that it would charge the first of its own soldiers for misconduct during its 22-day offensive in Gaza, a move seen as another concession to the international community and to the Obama administration.
In notable contrast to Netanyahu's earlier visit to the White House, the two men this time sat by the hearth of the Oval Office, speaking warmly of each other and of the tie between their countries.
That link is "unbreakable," Obama said, describing "the bond of two democracies who share a common set of values and whose people have grown closer and closer as time goes on."
As reporters watched, Netanyahu invited Obama to visit Israel. Obama smiled and replied, "I'm ready." No date was set.
As he completed his remarks, Obama reached over to Netanyahu for a protracted handshake before they went off for lunch together.
But the painstaking demonstration of civility may mask lingering tensions. Before they can make long strides toward direct peace talks, the two sides must hash out a host of serious differences.
Netanyahu endorsed the idea of a Palestinian state for the first time last summer, for example, but only on the conditions that any independent entity not be militarized and that the Palestinians recognize Israel as the state of the Jewish people.