WASHINGTON — The Senate voted on Thursday to end American military assistance for Saudi Arabia’s war in Yemen in the strongest show of bipartisan defiance against President Trump’s defense of the kingdom over the killing of a dissident journalist.

The 56-to-41 vote was a rare move by the Senate to limit presidential war powers and sent a potent message of disapproval for a nearly four-year conflict that has killed thousands of civilians and brought famine to Yemen. Moments later, senators unanimously approved a separate resolution to hold Crown Prince Mohammed bin Salman of Saudi Arabia personally responsible for the death of the journalist, Jamal Khashoggi.

Together, the votes were an extraordinary break with Mr. Trump, who has refused to condemn the prince and dismissed United States intelligence agencies’ conclusions that the heir to the Saudi throne directed the grisly killing.

While the House will not take up the measure by the end of the year, the day’s votes signal that Congress will take on Mr. Trump’s support of Saudi Arabia when Democrats take control of the House next month.