The vote is a victory for President Obama as Republicans had wanted to strip funding for the president's executive actions on immigration from the bill.
The Israeli premier's remarks are the culmination of a controversy that began in January when he was invited — without input from the White House — to make the speech.
The Israeli prime minister said his country has a "profound disagreement" with the White House on nuclear talks with Iran, and it is his duty to speak up on an issue that affects Israel's survival.
President Obama late Friday signed a stopgap measure to keep the department running for another week, but the tussle over his executive action on immigration, linked to the funding, is not over yet.
The Senate approved a bill that funded Homeland Security through Sept. 30. The Republican leadership in the House decided to move forward with a more limited bill, but that failed.
Senate Majority Leader Mitch McConnell, R-Ky., said the Senate will vote no later than March 3 to override the veto. But Republicans do not appear to have enough votes to override the veto.
The new Authorization for the Use of Military Force, or AUMF as it's known, bans the use of U.S. forces "in enduring offensive ground combat operations."