The vote makes the chances of a government shutdown Tuesday increasingly likely.
That’s because passage of the amendments sends a temporary budget resolution back to the Senate, where Democrats vow to again block the anti-Obamacare amendments.
President Barack Obama has added a veto threat to that position.
Without a deal, a government shutdown will begin at 12:01 a.m. Tuesday.
A Senate Democratic source told CNN there were no plans to convene the Senate before Monday, when the current fiscal year ends.
The decision to vote on the House amendments Saturday night emerged from a rare weekend GOP caucus meeting called by House Speaker John Boehner.
The votes, taken after midnight, were 232-192 for the Obamacare delay, and 248-174 for the medical device tax repeal, mostly along party lines.
Two Democrats voted for the Obamacare delay: Mike McIntyre of North Carolina, and Jim Matheson of Iowa.
Seventeen Democrats voted for the tax repeal.
Meanwhile, a bill to guarantee pay for military personnel during any shutdown passed 423-0.
Senate Majority Leader Harry Reid called the Republican strategy “pointless” and said the Democratic-led Senate would reject the GOP alternatives, while the White House said Obama would veto the House proposal if it reached his desk.
A separate White House statement said voting for the GOP measure “is voting for a shutdown.”
The partisan back and forth over the spending plan — called a continuing resolution in legislative jargon — came after the Senate on Friday restored funding for Obamacare that House Republicans stripped from their original version and sent the proposal back to the House.