The passage of the coalition's controversial NHS reforms would prove to be a "cause of significant regret", according to the Royal College of Nursing (RCN).
The bitter 14-month parliamentary battle finally came to an end on Tuesday night after the government comfortably fended off a desperate attempt by Labour to delay the legislation.
MPs then approved the last amendments to the Health and Social Care Bill - leaving the way clear for Royal Assent to be granted before Parliament starts its Easter recess next week.
The NHS shake-up has threatened to drive a wedge between the coalition partners ever since it was unveiled by Tory Health Secretary Andrew Lansley.
It is intended to give GPs greater control over NHS budgets, reduce bureaucracy, and increase patient choice.
But while there was jubilation among Tory and Liberal Democrat ministers, opponents have warned that the problems are only just beginning.
RCN chief executive and general secretary Dr Peter Carter described the reforms as "deeply flawed".
He said: "We have achieved some concessions which make the Bill a different piece of legislation from that which first appeared, but our real concerns about the future of the NHS have not been heeded.
"It is now our responsibility to patients to do everything we can to ensure that the health service runs as best as it can despite the massive upheaval that this Bill will bring.
"We intend to work with trusts, regulators and other bodies but our fear is that in the fullness of time this Bill will be a
cause of significant regret.
"Perhaps most importantly we will be supporting nurses who are going to have to pick up the pieces and still deliver the best care they can for patients through this extremely difficult time of change."
Furious opposition from professional bodies and Lib Dem activists led David Cameron and Nick Clegg to take the highly unusual step of "pausing" the legislation last year.
Despite accepting more than a thousand amendments - including limits on competition and private sector involvement - the Government has failed to win over many health workers.
Lib Dems embarrassed Clegg at the party's spring conference this month by again refusing to back the measures in a vote.
And there is speculation that the controversy could yet cost Lansley his job in a reshuffle expected over the coming months.
When the Cabinet met yesterday, ministers from both parties banged the table to celebrate news that the reforms had finally cleared the House of Lords.
An emergency debate called by Labour had the potential to delay the Bill until an internal assessment of risks had been published.
Shadow health secretary Andy Burnham demanded that the Government publish the risk register, insisting: "People outside will struggle to understand how Members of this House could make such momentous decisions without having carefully considered all of the facts and all of the evidence."
But Lansley accused Labour of "political opportunism", saying civil servants needed "safe space" in which to advise ministers.
The Commons defeated the motion by 328 to 246 - a majority of 82. No Lib Dem MPs sided with the opposition, with the most vocal critics choosing to abstain.
After the House agreed more than 370 amendments to formally pass the Bill later, Burnham insisted the "fight will go on" and promised to repeal the measures if Labour returned to power.
"We have given this fight everything that we had," he said. "All I can say is our fight will go on to protect and restore this party's finest achievement."