Saudi civil defence had issued several warnings for Yanbu, on the Red Sea, and later said the danger had passed.
Civil defence also issued a warning for the port city of Jizan about 1000km to the south, close to the Yemeni border.
Reuters verified video shared on social media of a large column of smoke rising from the direction of the Saudi Aramco refinery in Jizan. Two Asia-based trading sources said that they had been informed of some damage at the site.
The defence system was operated by Greek military personnel, the sources said. Greece has deployed a US-made Patriot air defence battery in Saudi Arabia since 2021 under an agreement to help protect the kingdom's energy infrastructure.
US President Donald Trump vowed "major military punishment" for Tehran and its Houthi allies in Yemen, after the Houthis said they had struck two Saudi tankers in the Red Sea on Thursday.
The Houthis, who control northern and western Yemen, have declared a naval blockade of Saudi Arabia. The kingdom has been diverting millions of barrels of oil by pipeline each day to the Red Sea to skirt Iran's near-total blockade of the Strait of Hormuz on the Gulf.
Two weeks after the collapse of an interim truce meant to end the war, the Iranian armed forces responded by firing at US bases in neighbouring Arab countries overnight and warned people there they could strike non-military buildings used by US personnel.
Trump has in recent days threatened to expand the targets being struck in Iran to include energy plants and bridges, to send ground forces to seize its Kharg Island oil hub and to bomb a deep-underground nuclear-linked site known as Pickaxe Mountain.
On Friday, he said he had not yet made a decision for new major strikes.
"We are talking to them. I think they're being serious. I think ... they are being by far the most serious that we've seen them, but that doesn't mean we get there," Trump told reporters at the White House.
Asked what is the exit strategy for the Iran war, he said: "There's a military exit where we just keep going just the way we are, and we can even make it a heavier dose, and it's knocking out everything they have. Or there's a smarter strategy that you make a deal."
But he added: "We're locked and loaded. We're ready to go."
The entrance to the Gulf has so far been the focus of a war that has killed thousands of people in almost five months, stoked global inflation and fanned fears of an economic downturn.
The Houthis, who control northern and western Yemen, have announced a naval blockade on Saudi Arabia, which has diverted millions of barrels of oil each day by pipeline to the Red Sea to skirt Iran's near-total blockade of the Strait of Hormuz.
On Friday, several strikes hit Yemen's Hodeidah port, eyewitnesses said. The Saudi-led coalition in Yemen said it carried out a "proportionate military response operation" that targeted Houthi military sites in Hodeidah governorate.
The US military launched air strikes on Iran late on Thursday and early on Friday, for a 13th consecutive night of attacks, prompting Iran to fire at neighbouring Arab countries that host US bases.
In a statement on X, the Iranian health ministry said 59 people had been killed and 666 wounded since the resumption of clashes with US forces in late June.
Iranian media cited the head of Iran's top joint military command as saying Iran would kill a member of the US forces for every Iranian killed. The war has killed 18 US service members.
The Pentagon said on Monday 100 service members had been injured since July 7 and 96 per cent have returned to duty. Officials have told Reuters that more than 500 US troops have been injured so far.
