He thanked Justice Christine French and bowed in the dock as she told him he was free to go.
"Now we can sit down and remember our daughter,'' Mr Gwaze said on the High Court steps in Christchurch, after being acquitted.
Mr Gwaze thanked his friends and family for all their support over the past five years and said he was always confident of being found not guilty.
"I was (confident) because of `beyond reasonable doubt' - those few words work wonders and it makes a jury think. I knew there was nothing that happened to our daughter.''
He said he was "relieved'' but at ease and composed before the verdict was reached.
The Zimbabwean immigrant said he would remain living in New Zealand, despite the ordeal.
He also thanked his legal team, and paid special tribute to his lawyer, Jonathan Eaton.
"He is a great man and I think he'll be a family friend for life.''
Mr Eaton said today was important in New Zealand's legal history.
"It's been an extraordinary long road. I don't know anybody in our legal history who has stood on these court steps having been acquitted twice.
"The Gwaze family have been through the ringer with the judicial system.''
Mr Eaton said the verdict was very rewarding and "satisfying'' for his client.
The lawyer ruled out making calls for a investigation into the police handling of the case, saying they were only acting on expert medical advice.
"It wasn't the police making the black and white calls about what happened,'' he said.
"Our defence was very much structured around not attacking the police but attacking that medical opinion, and I felt that with the invaluable assistance from four very experienced experts from overseas, it created more than reasonable doubt in this case.
"That is really where the questions will ultimately be asked about where this case went off the rails.''
Charlene's cousin, and the Gwazes' 27-year-old daughter Nothando Musesengwa said it was the "only verdict we were expecting''.
"We've had so much peace of mind knowing the truth,'' the law student said.
She told APNZ the family were relieved, and "over the moon'' at the decision but admitted the process had been "rough''.
"Ever since January 7, 2007, our life hasn't been normal.''
She said her father had been "a rock'' for the family, and stoical throughout. The trials, however, had taken "a really hard toll'' on her mother.
"It's been hard on mum because she's had to work extra because dad hasn't been working. She has developed diabetes. She is fine but it's been rough.
"We haven't had time to grieve for Charlene, but now we can do that.''
Second trial ends in acquittal
It is the second time that Gwaze has been acquitted for the rape and murder of 10-year-old Charlene.
After a High Court trial in 2008, he was acquitted of the charges.
The Crown unsuccessfully appealed the jury's original not guilty verdicts at the Court of Appeal.
But in a legal first, the Supreme Court quashed Gwaze's acquittals last year and ordered a retrial.
Justice French today thanked the jury for their efforts.
Not even a 5.2 magnitude earthquake last Friday stopped the jury from deliberating over their decision.
The Crown had alleged that Charlene, who had HIV, was sexually attacked and suffocated by her uncle who she knew as "dad''.
Traces of Gwaze's DNA was found on Charlene's clothing and bedsheets, but no traces were found on the girl herself.
DNA profile expert Susan Vintiner gave evidence warning that the scientific discoveries should be treated with caution, saying that normal household washing cycles "really changes everything'' when it comes to weighing up DNA finds.
Mrs Gwaze found Charlene unresponsive in her bed at the family home in Bryndwr, in Christchurch, at 5.45am on January 6, 2007.
Mrs Gwaze had gone into her room, which she shared with her 27-year-old cousin Nothando, after hearing abnormal "loud breathing''. The 57-year-old rest home night-shift worker said she found Charlene covered in diarrhoea.
The family drove her in the back seat of their car to a 24-hour medical centre in Christchurch, before being rushed to the city's public hospital.
After being seen in the emergency department, she was taken to a trauma room where "a lot of doctors'' worked on the dying girl.
They also feared she might have meningitis, and told the Gwazes she would be transferred to Starship Children's Hospital in Auckland where she would receive specialist treatment.
Only two family members could go with her, so Mrs Gwaze said she would go, along with her son Tafadzwa, who was "very close'' with Charlene - the "baby'' of the family.
But the Christchurch medical team found her quickly condition deteriorated, and also found she was HIV positive.
She died the next day.
Gwaze's defence team argued the girl - a "quiet and sweet little girl'' who was often too unwell to go to school, and had to be showered, dressed, and fed by her aunty Sifiso - was "riddled'' with the HIV she had carried since birth, and that was what killed her.
Charlene's birth mother - Mrs Gwaze's younger sister - died of tuberculosis in Zimbabwe in 1998.
The girl's father died two years later and, despite having four children with Mr Gwaze and another from a different relationship, Mrs Gwaze took 5-month-old Charlene and her older sister Charmaine into her care.
Mrs Gwaze said that the family adapted to cope with living with Charlene, who had more needs than the other children.
Gwaze, a former vet to the Zimbabwean government who migrated to Christchurch in 2005 to escape the Mugabe regime, had worked in Christchurch at a lab technician.
The rest of the family followed him to Christchurch over the next few years.
The court was told that Charlene found going to the toilet "painful''. The family said they did not know she was HIV positive until the day she was taken to hospital.
Mr Eaton earlier told the jury that his client was a kind and loving family man and that no crime had been committed.
He said it was utterly inconceivable his client would commit the "vicious, violent and heinous assault''.
The Crown case was so "bizarre, illogical, and inexplicable'', he said, that there had to be another explanation - and that was HIV.
Mr Eaton suggested the Crown and its experts had "closed their minds'' and were not interested in exploring alternatives for Charlene's injuries.
Detective Senior Sergeant David Harvey, officer in charge of the retrial, said police would not be making any comment on the verdict, but did acknowledge the difficult time Charlene's families have been through.
"They have been through a great deal during the investigation and prosecution over the past five years, and we again express our sympathy to them over the loss of Charlene," Mr Harvey said.
"I also acknowledge the exemplary medical treatment that Charlene received from medical staff, both at the Christchurch 24-Hour Surgery and at Christchurch Hospital's Emergency Department and Intensive Care Unit.
"The expertise and assistance of a large number of specialists and expert witnesses has also been highly valued by Police over the course of this and previous prosecutions."
