The Democratic-led Senate has blocked an effort to strip money from the president's health care law.
The party-line, 54-44 vote clears the last obstacle to Senate approval of a measures aimed at preventing a government shutdown on Tuesday.
The Republican-run House had included the Obamacare language in its version of the shutdown bill at the insistence of conservatives.
A small group of Senate conservatives tried but failed to stop the Senate from considering the bill. They argued their strategy would have kept Democrats from removing the Obamacare provision.
Still unclear is whether Congress will approve legislation preventing a shutdown by Tuesday.
House GOP leaders have yet to determine how to win enough conservative support to pass a new bill.
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