Expressing "deep sympathy" for the families of the victims, Obama said the law would be "detrimental to US national interests."
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The White House tried and failed to have the legislation - which was unanimously backed in Congress - from being substantially revised.
Obama now faces the prospect of Republican and Democratic lawmakers joining forces to override his veto for the first time in his presidency.
Such a rebuke would overshadow his last months in office and show the White House to be almost fatally weak.
New York Senator Chuck Schumer, a Democrat and cosponsored the bill, said he would press ahead with the override.
"This is a disappointing decision that will be swiftly and soundly overturned in Congress."
"If the Saudis did nothing wrong, they should not fear this legislation. If they were culpable in 9/11, they should be held accountable."
Families of 9/11 victims have campaigned for the law - convinced that the Saudi government had a hand in the attacks that killed almost 3,000 people.
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Fifteen of the 19 hijackers were Saudi citizens, but no link to the government has been proven. The Saudi government denies any links to the plotters.
Declassified documents showed US intelligence had multiple suspicions about links between the Saudi government and the attackers.
"While in the United States, some of the 9/11 hijackers were in contact with, and received support or assistance from, individuals who may be connected to the Saudi government," a finding read.
Behind the scenes, Riyadh has been lobbying furiously for the bill to be scrapped.
A senior Saudi Prince reportedly threatened to pull billions of dollars out of US assets if it becomes law, but Saudi officials now distance themselves from that claim.
The US-Saudi relationship had already been strained by Obama's engagement with Saudi's Shia foe Iran and the July release of a secret report on Saudi involvement in the attacks.
The White House insists Obama did not veto because of Saudi Arabia, saying it is worried the bill would set a dangerous legal precedent, undermining the principle of sovereign immunity.
The European Union and a host of countries have expressed similar concerns.
But that technical legal argument will struggle to be heard over emotive accusations that Obama is putting relations with Saudi Arabia before 9/11 victims.
Republicans will certainly use the veto to cast Obama as putting monarchs in Riyadh before US terror victims.
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The Republican nominee, Donald Trump has already tried to paint Obama and his would-be successor Hillary Clinton as weak on terrorism.
The White House will now hold out hope that convoluted Congressional rules could delay the override until after the November 8 election, when the politics may be less toxic and minds may be changed.
Congressional sources said White House appeals to security minded senators like Dianne Feinstein may yet be enough to avoid an override vote.
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