In a landmark 97-1 vote backing the override, only outgoing Obama ally, Nevada Democrat Harry Reid, voted against it, teeing up a similar vote in the House of Representatives later today.
The rare act of bipartisanship is a severe blow to Obama, who lobbied hard against the bill, known as the Justice Against Sponsors of Terrorism Act (JASTA).
The rebuke marks Obama's last months in office and shows the White House to be much weakened.
His Republican predecessor George W Bush also issued 12 vetoes and four were overriden. The last president to avoid an override was legendary Democratic congressional dealmaker -- and former senator and congressman -- Lyndon Johnson.
The White House argued the 9/11 bill would undermine the principle of sovereign immunity and open up the United States itself to lawsuits.
In a letter to Republican and Democratic Senate leaders obtained by AFP, Obama said: "I strongly believe that enacting JASTA into law would be detrimental to US national interests."
It would "neither protect Americans from terrorist attacks, nor improve the effectiveness of our response to such attacks," he warned.
"The United States relies on principles of immunity to prevent foreign litigants and foreign courts from second-guessing our counterterrorism operations and other actions that we take every day."
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.
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.
"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.
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