He also assured King Abdullah that the US "won't accept a bad deal" with Iran, as global powers negotiate a treaty reining in Tehran's controversial nuclear programme.
Obama arrived from Italy to meet for some two hours with the monarch of the oil-rich kingdom on a royal estate outside Riyadh on the last leg of a six-day tour.
The US president told the king that "he believes that our strategic interests remain very much aligned" with those of Saudi Arabia, a senior US administration official told reporters.
"One of the main topics of conversation" would be "how do we best empower the moderate opposition inside of Syria politically, militarily as a counterweight to (President Bashar) Assad," deputy national security advisor Ben Rhodes told reporters on board Air Force One.
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"Our relationship with the Saudis is in a stronger place today than it was in the fall (autumn) when we had some tactical differences about our Syria policy," he said.
But officials shot down as untrue reports that the US administration was planning to give Riyadh a green light to ship heavy weapons, known as MANPADs, to the beleaguered moderate Syrian opposition.
"We have not changed our position on providing MANPADS to the opposition," a second senior administration official said, acknowledging "this is a proliferation risk".
"This wasn't a focus of the meeting," he insisted.
Riyadh also has strong reservations about revived efforts by Washington and other major world powers to negotiate with Iran.