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The top US diplomat was hastily dispatched to Riyadh to patch things up after rare complaints from Riyadh over Washington's policies on Syria and Iran.
"Our relationship is strategic, it is enduring and it covers a wide range" of issues, he told reporters as he wound up a visit, including a two-hour meeting with King Abdullah.
He insisted the two allies agreed on the "goal in Syria".
"There is no difference in our mutually agreed upon goal in Syria," Kerry told a joint news conference with his Saudi counterpart, Prince Saud al-Faisal.
He insisted Washington "will not stand idly by as (Syrian President Bashar al-) Assad continues to use weapons" against his own people.
But Prince Saud, while stressing the strength of ties with the United States, slammed the "international community's failure to stop the war against the Syrian people".
Negotiations to solve any crisis "shouldn't just go on indefinitely", he said in reference to a US-Russian proposed peace conference.
He insisted that some "grave issues desperately need decisive and resolute intervention that should put an end to the human tragedies they produced".
Saudi Arabia expressed anger after US President Barack Obama stepped back after threatening a punitive strike against Syria over a chemical attack in August on a rebel-held district near Damascus.
Kerry reiterated that Washington opposes military intervention to end the 31-month conflict.
"Absent a negotiated solution we don't see a lot of ways to end the violence that are implementable or palatable to us, because we don't have the legal authority, or the justification or the desire at this point to get in the middle of a civil war," he said.
"I think that's been made very, very clear," he added.
"Our hope is we can bring the parties together. It won't be the first very complicated conflict, where very emotional highly separate entities are brought together by an international community and ultimately find their way forward," he said.
Kerry earlier acknowledged things were tough as the region is rocked by the turmoil of the Arab Spring, which is reshaping the geopolitical landscape.
"Right now we have some very important things to talk about to make certain the Saudi-US relationship is on track, moving forward and doing the things that we need to accomplish," he told US embassy staff in Riyadh.
Saudi Arabia, locked in a decades-long rivalry with Iran, is concerned that proposed Syrian peace talks could leave a Tehran-backed regime in place in Damascus and that a breakthrough in nuclear negotiations could also lead to a US rapprochement with its arch-foe.
Prince Saud accused Iran of occupying Syria by dispatching fighters and prodding Lebanon's Shiite Hezbollah movement to fight the rebels.
"Syria is a land occupied by Iranian forces," he told reporters.
"The best test for Iran to prove its goodwill would be its withdrawal from Syria along with its Lebanese Hezbollah ally," he added.
Kerry praises Saudis
Kerry paid tribute to the conservative oil-rich kingdom's traditional role in the region, praising the Saudis as "really the senior player in the Arab world".
Washington and Riyadh shared many current concerns, he said, highlighting the difficult transition in Egypt, the war in Syria and Iran's nuclear ambitions.
He repeated US assurances that Iran "will not get a nuclear weapon" after stressing a day earlier, in a veiled warning to Tehran, that Washington would stand by its Arab friends.
In an unprecedented move last month, Saudi Arabia turned down a coveted non-permanent seat on the UN Security Council in protest at the world body's failure to end the war in Syria, which has killed more than 120,000 people.
Saudi intelligence chief Prince Bandar bin Sultan al-Saud also reportedly told diplomats last month he would scale back cooperation with the CIA on training Syrian rebels.
Kerry's 11-day tour comes at the start of a key week, with talks scheduled in Geneva on trying to fix a date for the Syria peace talks and a new round of nuclear negotiations between six world powers and Iran.
Riyadh has also eyed warily international moves to engage Iran on its nuclear programme following the election of President Hassan Rouhani, a reputed moderate who held a landmark phone call with US President Barack Obama in September.
Analysts said while ties between the US and Saudis are strained they are unlikely to break completely.
"Despite the Saudi outcry, the bedrock of US and Saudi ties -- intelligence coordination and military containment of Iran -- is solid," wrote Frederic Wehrey of the Carnegie Endowment for International Peace.