The legislation no longer contains the universal healthcare option Obama initially proposed.
And even this stripped-down version - which passed along partisan lines - is facing political challenges.
The US senate must still pass a reconciliation or "fix-it" bill that would detail how to pay for healthcare overhaul.
Republican politicians are also promising to use a number of parliamentary objections to try and stall its passage in the senate, and are threatening to undo the measure.
The approval fulfils a goal that had eluded many US presidents for a century - most recently Bill Clinton in 1994.
Republican critics said the legislation was a heavy-handed intrusion in the healthcare sector that will drive up costs, increase the budget deficit and reduce patients' choices.
They also say they would fight a package of changes designed to improve the bill, which will be taken up in the senate this week, and lead a charge to repeal the bill after reclaiming congress from the Democrats in November's elections.
"We will challenge this all over America, and the will of the people will be heard," John McCain, a Republican senator and 2008 presidential contender, said.
Republicans said they would challenge the changes to the overhaul on parliamentary points of order that, if upheld, could send the revisions back to the House.
At least 13 states, including Florida, Michigan and Alabama, plan to come together in a collective lawsuit claiming the reforms infringe on state powers.
Rob Reynolds, Al Jazeera's correspondent in Washington, said: "So far, 13 state attorney-generals ... have announced they are going to challenge the bill on constitutional grounds.
"They say it is a seizure of too much power by the federal government.
"And so that fight will play itself out in federal and state courts and probably go all the way to the supreme court, and so this fight is not over yet."
Obama was at his lowest point in public opinion polls, 15 months into his presidency, and there were questions about whether he would be able to accomplish anything on his domestic agenda if he could not get the healthcare bill passed.
The passage of the bill was also a victory for Democrats, who can now cite it as an accomplishment when they face voters in midterm congressional elections in November.
However, some critics have said that the legislation does not go far enough, pointing out that millions of people will still be without health insurance under the system.
Matt Hendrickson, a California doctor and member of Physicians for a National Health Program (PNHP) said: "What it's doing is transferring half a million dollars to the private insurance industry.
"It will enrich and entrench the private insurance industry in what is the fundamental flaw of the American healthcare system, that it is a for-profit private insurance base model that can't cover all Americans and can't control costs," he told Al Jazeera.
"At least 23 million people will remain uninsured, although that number will probably grow because as we've seen in the Massachusetts model and in several other state models the initial attempt to subsidise those that can't afford the insurance slowly diminishes because the costs are not controlled and the government can no longer keep up with the rising costs."