The minister had come under pressure to review the proposals unveiled last week.
There had been a mixed response from the British Medical Association, GPs and opposition parties who said the proposals would mean more bureaucracy and more expense with no more treatment for patients.
But addressing the chamber on Thursday, she said she would stick to her original, complex plan of abolishing the exisiting five NHS authorities to make way for 22 local health boards.
Mrs Hutt said the aim was to strengthen local health bodies and she argued that it was not a "cost-driven" reorganisation.
"In discussions, people have been saying this is the way forward. Community Health Councils back these proposals," she said.
"It is about patients, nurses and GPs."
In what is perceived as a concession to the Liberal Democrats, the role of the existing Specialised Health Services Commission will be strengthened.
She said the commission, which currrently buys highly specialised services, will also provide dedicated guidance to the new partnerships and health board on the purchasing of hospital services.
Plaid Cymru's spokesman on health, Dr Dai Lloyd, criticised the plan and repeated his party's demand for an all-Wales commissioning authority.
"I'm aghast," he told the chamber.
"I was expecting, following the Lib Dem revelations that we were going to have some magnificant new proposals, that things would be transformed. But obviously not."
"Nine months and nine task forces got us to last week's proposals, complex as they were, even more complex now and expensive.
Tory health spokesman David Melding dismissed the changes as a "disaster".
Nothing, he said, had fundamentally changed and that another body has been added to the already Byzantine structure "in a vain attempt to make the unworkable last a bit longer".
There was a warmer welcome for the changes from Labour's coalition partners in the assembly, the Liberal Democrats.
Health spokesman Peter Black said his party's approach to the NHS structural reform was based on the same principles - the wish to strengthen the local partnerships, and the wish to strengthen the all-Wales strategic approach to commissioning health services.
Last week, the party was understood to have been annoyed by Ms Hutt's original plans and a last-minute revised deal was understood to have been struck between the two parties late on Wednesday.
Hitting out at the "distortion" of events in the media, Ms Hutt urged AMs "to have confidence in the people who are working in the health service because they are the ones who are going to implement them (the changes)".
Independent Conservative Rod Richards asked if the health minister realised everyone had lost confidence in her.
"Does the health minister now realise that she has lost the confidence of the assembly, that she has lost the confidence of the health commitee, that she has lost the confidence of the NHS but most importantly, that she has lost the confidence of NHS patients?" he said.
The plans will now be debated at a plenary session of the assembly on 27 November.