The Senate voted largely down party lines in removing the Obamacare amendment, as well as a provision that would have eliminated the tax on medical devices.
House Republicans had added the provisions early Sunday.
The Senate vote came less than 10 hours before the US government was scheduled to shut down for the first time since 1995.
According to Politico and the Washington Post, House Republicans now plan to propose a bill funding the government but delaying the individual mandate portion of Obamacare, rather than the entire health care reform law.
If that happens, a shutdown seems all but certain given Senate Democrats' opposition to any Obamacare provisions in the spending bill.
Meeting with Israeli Prime Minister Benjamin Netanyahu, President Barack Obama told reporters he is "not at all resigned" to a shutdown.
"The bottom line is that the Senate has passed a bill that keeps the government open, does not have a lot of extraneous issues to it, that allows us to then negotiate a longer-term budget ... but ensures that we're not shutting down the government ... at a time when a lot of families" are just now digging themselves out of hard times, he said.