The vote took place after the White House issued its expected veto threat against the bill, and after an angry House debate in which Democrats accused some Republicans of looking to starve the government of funding.
Hoyer's criticism mirrored that of other Democrats, who said linking the spending bill to language defunding ObamaCare is reducing the chances that Congress can keep the government open after September.
But Republicans rejected that charge, and said the resolution includes several Republican priorities, one of which is to keep the government open.
"Some have said that this is just brinkmanship and an attempt by Republicans to lead to a government shutdown," Rep. Tom Cole (R-Okla.) said. "That could not be further from the truth. The Appropriations Committee has brought this bill the floor explicitly to avoid the threat of a shutdown."
While many say the GOP bill appears to be designed to create a government shutdown, Cole said it reflects a GOP effort to use regular order to pass a funding bill. He said once the House passes it, the Senate should make its own adjustments and send it back to the House.
"We'll send this over to the Senate, we'll see what our colleagues can do over there," Cole said. "Once they've made their decision … then they'll send something back. And at that time, I have no doubt that we'll pick it up and react to it and try to respond in appropriate fashion."
Cole said Republicans support the bill because it would continue the sequester policy that cut $80 billion from federal spending and defund ObamaCare. It would also require the Treasury Department to prioritize interest payments on the debt in the event of a government shutdown.
The ObamaCare and debt payment prioritization language was automatically included in the resolution when the House approved the rule. House aides explained on Wednesday that the language was "self-executed" by passage of the rule.
Earlier on Thursday, the Congressional Budget Office said it was unable to estimate the cost of the language defunding ObamaCare.
Democrats indicated that continuation of the sequester cuts is another reason why they oppose the bill.
"The sequester has been one of the most devastating policies ever implemented in the history of the United States," said House Rules Committee ranking member Louise Slaughter (D-N.Y.).
House Agriculture Committee ranking member Collin Peterson (D-Minn.) voted against the CR and predicted that only one or two Blue Dog Democrats would support it. He said he still has some concerns about ObamaCare, but threatening a shutdown is going too far.
"This is not the way to do business," he said after the vote. "I've never been for repealing it because I'm a big supporter of the exchanges."
— Erik Wasson contributed.