The Senate had previously passed the bill 81-18. It now heads to the White House, where President Obama has said he would sign it.
Upon Obama's signature, the first government shutdown in 17 years will end after 16 days.
The bill funds the government through Jan. 15 and raises the debt ceiling until Feb. 7. It calls for a House-Senate conference committee that must report budget recommendations by Dec. 13.
The Obama administration will be required to verify that people seeking tax subsidies to buy insurance under Obamacare have an income level makes them eligible for assistance under the law.