The measure marks halfway point in the House's consideration of fiscal appropriations.
Nevada lawmakers tried to block construction of a nuclear repository in their state.
The Speaker made clear that strings will be attached to the funding Obama requested.
Speaker Boehner called off the morning session because of a potential asbestos leak.
The House will continue consideration of the fiscal 2015 Energy-Water appropriations bill, while the Senate will consider the nomination of Shaun Donovan to lead the Office of Management and Budget.
The measure to streamline jobs programs passed the House 415-6 and the Senate 95-3.
The House on Wednesday rejected 110-310 a proposal to eliminate all funding for Department of Energy programs to promote energy efficiency and renewable energy.
The Georgia Republican will replace incoming House Majority Whip Steve Scalise.
Rep. Mo Brooks (R-Ala.) on Tuesday argued that illegal immigrants are causing income inequality in the U.S.
The Speaker said a "really solid bill" would help pay for the shortfall through early 2015.