The three-day visit is Obama's first to Israel and the Israeli-occupied West Bank since entering the White House in 2009, and the inaugural foreign trip of a second and final four-year term that began in January.
Sporadic protests flared in the West Bank and Gaza Strip this week, with Palestinians accusing Obama of not doing enough to halt Israeli settlement-building on land seized in the 1967 Middle East war.
In 2009, Obama bluntly told Israel it had to halt settlement construction, but he later backed away from the demand and made no mention of the enclaves on Wednesday.
Posters depicting Obama were defaced in the West Bank cities of Ramallah and Bethlehem earlier this week and anti-U.S. sentiment bubbled up on social media.
"Do Not Enter," said one poster put up on Facebook, showing Obama's face with a red line crossed through it. "The people of Palestine do not welcome you here."
Obama was feted when he arrived at Tel Aviv airport on Wednesday, with Israeli leaders lining up to praise the U.S. president for his firm commitment to the security of the Jewish state and his pledge not to let Iran develop nuclear weapons.
Netanyahu, while citing what he described as Israel's right to defend itself, said effusively that he was "absolutely convinced" that Obama was determined to prevent a nuclear-armed Iran. Tehran says it is enriching uranium for peaceful purposes.
After four years of often icy relations with Netanyahu, the body language suddenly changed. Gone were the pursed lips and ill-disguised scowls. In came firm handshakes and back-slapping.
"Israel has no better friend than the United States of America," Netanyahu said, adding that he hoped his visit would help "turn the page" in relations with the Palestinians.
"Israel remains fully committed to peace and to the solution of two states for two peoples. We stretch out our hand in friendship to the Palestinian people," he added.