The re-authorisation secures what supporters call a key element of US foreign intelligence gathering.
"Democrats and Republicans came together and did the right thing for our country safety," Senate Majority Leader Chuck Schumer said.
"We all know one thing: letting FISA expire would be dangerous. It's an important part of our national security, to stop acts of terror, drug trafficking and violent extreme extremism."
White House national security adviser Jake Sullivan said the legislation was one of the United States' most vital intelligence collection tools, and Biden would sign it quickly.
Section 702 of the Foreign Intelligence Surveillance Act, or FISA, is one of a suite of authorisations passed after the September. 11, 2001 attacks that allow US spy agencies to surveil foreigners abroad using data drawn from US digital infrastructure such as internet service providers.
The information is used to track enemy spies, rogue hackers and extremist militants.
FISA has attracted criticism from both Republican and Democratic lawmakers, who argue it violates US citizens' constitutional right to privacy.
The bill was blocked three times in the past five months by House Republicans bucking their party, before passing last week by a 273-147 vote when its duration was shortened from five years to two years.
The White House, intelligence chiefs and top lawmakers on the House Intelligence Committee have said not re-authorising the program could have potentially catastrophic effects.
Although the right to privacy is enshrined in the US constitution, foreign citizens' data gathered by the program often includes communications with US citizens, and can be mined by domestic law enforcement bodies such as the FBI without a warrant.
That has alarmed both libertarian Republicans and progressive Democrats.
Recent revelations that the FBI used this power to hunt for information about Black Lives Matter protesters, congressional campaign donors and US lawmakers have raised further doubts about the program's integrity.
