Lawmakers voted 230-189, largely along party lines, in support of the so-called continuing resolution that funds government operations at current levels up to December 15.
Many federal agencies and programmes will shutter on October 1, day one of the coming fiscal year, if Congress and the president do not agree on a temporary budget measure.
But the Republican bill, in a nod to the party's more conservative wing, includes a provision that strips funding for the health care law, which the GOP has fought to repeal virtually since its passage more than three years ago.
Inclusion of the controversial provision, however, virtually assures that the bill will not become law.
Senate leader Harry Reid has promised defeat of the measure in the Democrat-run chamber, saying yesterday that "any bill that defunds Obamacare is dead here."
The term "Obamacare" was coined by Obama's critics to describe the health care law.
Reid has signaled he would seek to strip out the provision and approve a clean funding bill next, sending it back to the House with little room for maneuver.
