An earlier compromise proposed by Boehner and fellow GOP House leaders to their conservative wing would have allowed a symbolic vote on the defunding provision that the Senate would then strip out.
The result would have been what legislators call a "clean" final version that simply extended current levels of government spending for about two months of the new fiscal year, allowing time for further negotiations on the debt ceiling.
However, conservative opposition to the compromise made Boehner agree to a tougher version that made overall government funding contingent on eliminating money for Obamacare.
Moderate Republicans question the strategy, but fear a right-wing backlash in the 2014 primaries if they go against the conservative wing.
In reference to the divisions in the House, McCain said it is "pretty obvious that (Boehner) has great difficulties within his own conference."
On the House floor on Friday, legislators warned of the serious consequences of a government shutdown. The last shutdown, which occurred during the Clinton administration more than 17 years ago, comprised a total of 28 days and cost the nation more than $1 billion, according to congressional researchers.
House Democratic leader Nancy Pelosi of California said the intent of the Republican measure is to shut down the government, calling it a "wolf in wolf's clothing."
GOP Rep. Harold Rogers of Kentucky, who chairs the House Appropriations Committee, said "a government shutdown is a political game in which everyone loses."
"It shirks one of our most basic duties as members of Congress and it puts our national security at stake," he added.
Republicans said the House vote showed bipartisan support for defunding Obamacare because two Democrats backed the GOP resolution -- Reps. Jim Matheson of Utah and Mike McIntyre of North Carolina.
Meanwhile, Rep. Scott Rigell of Virginia was the lone Republican to break ranks with his caucus by voting against it.
In the Senate, Majority Leader Harry Reid of Nevada made clear on Thursday that any plan to defund Obamacare would be dead on arrival. Instead, the Senate is expected to strip the measure of all provisions defunding Obamacare and send it back to the House.
"They're simply postponing an inevitable choice they must face," Reid said of House Republicans.
Boehner would then have to decide whether to put it to a vote, even though that could undermine his already weakened leadership position by having the measure pass with only a few dozen moderate Republicans joining Democrats in support.
If he refuses to bring the Senate version to the floor for a vote, a shutdown would ensue.
"Will he act as the captain of the entire House of Representatives or remain a captive of his right wing Republican mates?" asked Democratic Rep. Sander Levin of Michigan. "Will he, as he acts, worry mainly about the risk to his speakership or the risk to our entire nation? House Republicans taking the ship over the cliff would take the nation's economic well-being with it."
Polls showing a decrease in public support for the health care reforms embolden the Republican stance. Meanwhile, Democratic resolve is bolstered by surveys showing most people oppose a government shutdown and more would blame Republicans if it happens.
Voices across the political spectrum warn against a shutdown, including Congressional Budget Office Director Douglas Elmendorf, Federal Reserve Chairman Ben Bernanke, the U.S. Chamber of Commerce, and Republican strategist Karl Rove.
"Even the defund strategy's authors say they don't want a government shutdown. But their approach means we'll get one," Rove argued in an op-ed published Thursday by the Wall Street Journal.