He described the bill as "an unnecessary, risky attempt to weaken my constitutional authorities, endangering the lives of American citizens and fearless service members".
It marked the first time both chambers of Congress had supported a War Powers resolution, limiting the president's ability to send troops into action.
"With Trump's veto of Bernie Sanders' and my War Powers resolution, he is risking the lives of millions of Yemeni civilians to starvation, deadly airstrikes, and the war crimes of the Saudi regime".
The U.S. provides billions of dollars of arms to the Saudi-led coalition fighting against Iran-backed rebels in Yemen.
In a statement Tuesday night, Pelosi called on Trump to "put peace before politics".
"It should come as a surprise to nobody", the official said.
Democratic Rep. Eliot Engel of NY, chairman of the House Foreign Affairs Committee, voted to end United States military assistance to the war, saying the humanitarian crisis in Yemen triggered "demands moral leadership".
USA senators have accused Saudi Crown Prince Mohammed bin Salman of ordering the murder of Mr Khashoggi, but Saudi prosecutors have insisted it was a "rogue operation" and that the agents were not acting on his orders.
Trump added that the resolution is "unnecessary" in part because there are no United States military personnel in Yemen "commanding, participating in, or accompanying military forces of the Saudi-led coalition against the Houthis in hostilities in or affecting Yemen". Congressional engagement in those endeavors would be far more productive than expending time and effort trying to enact this unnecessary and risky resolution that interferes with our foreign policy with respect to Yemen.
Rep. Ro Khanna (D-Calif.), who helped lead the House effort to end US military involvement in Yemen, denounced Trump's veto on Twitter.
In his State of the Union address in February, Trump declared, "Great nations do not fight endless wars".
He stated continued involvement was also necessary to 'protect the safety of the more than 80,000 Americans who reside in certain coalition countries'.
He also urged members of Congress to instead focus their energies on the drawdown of US troops in Afghanistan and Syria.
The California Democrat said that he will continue to push for a peaceful resolution to the conflict in Yemen and will continue to push for ending America's support in the war through future bills such as the National Defense Authorization Act (NDAA).