Judge Jeanette Traverso said the evidence presented by the prosecution fell "far below the threshold" of what a reasonable court could convict on.
She said the evidence of the prosecution's main witness was "riddled with contradictions".
Anni's family said they had been failed by the justice system.
Announcing her ruling, the judge said the only reason not to grant the application would be in the hope that Mr Dewani would implicate himself if he gave evidence.
But to do so would be a "manifest misdirection", she said.Mr Dewani, from Bristol, was extradited to South Africa this year to face trial accused of planning the murder of his wife in November 2010.
He listened intently as key evidence against him was criticised by the judge as she gave her ruling over almost three hours.
Mr Dewani, 34, went straight down to the cells to prepare for his release, following the decision, as his family embraced.
It is believed he left the court, without making a comment, through a side entrance.
Mrs Dewani's family, who had said it would it be a "nightmare" if the trial did not continue, immediately left the court room.
They bowed their heads amid shouting from the public gallery.
Speaking outside the Western Cape high Court, Mrs Dewani's sister Ami Denborg said: "Today we feel as a family that the justice system has failed us and we are deeply disappointed.
"We came here looking for answers and we came here looking for the truth and all we got was more questions.
"We waited patiently for four years to hear what really happened to Anni and to hear the full story of what happened to our dearest little sister.
"All we wanted was to hear all the events and the hope of actually finding that out has kept us, as a family, going.Unfortunately we believe that this right has now been taken away from us."
Her uncle, Ashok Hindocha said the family would be going through the case with their lawyers to confirm whether they can file a lawsuit against Mr Dewani in the UK.
"We would have preferred to have known about his sexuality before he married our precious Anni," he said.
"She gave herself to him, mind, body and soul and she hoped to have been cherished and loved. But she would not have married him if she had known about his secret sex life with male prostitutes and the activities he engaged in."The judge ruled it was not necessary for Mr Dewani to give evidence, saying a defendant was entitled to be discharged if there was no possibility of conviction unless he entered the witness box and incriminated himself.
The judge said the evidence from the three criminals already convicted over Mrs Dewani's murder was "so improbable, with so many mistakes, lies and inconsistencies you cannot see where the lies ended and the truth begins".
Dewani, 34, has always denied plotting with others to murder his bride, who was found shot dead in the back of their taxi after the couple were hijacked during a late-night tour of a township.Prosecutors said bisexual Mr Dewani had long planned to get out of the relationship to Swedish-raised Anni, and arranged the attack in which he would escape unharmed and Anni would be killed.
Judge Traverso said it was crucial for the state's case to prove that Mr Dewani entered into an agreement with others to have Anni killed.
Tongo was the only accomplice witness, she said, adding that such evidence should be treated with "caution".
Tongo's version needed to be corroborated specifically where it implicated the accused, she said.
Details such as where he picked up and dropped off Mr Dewani and his wife did not provide corroboration, the judge said.It is what was said during these events which is at issue and for that there is only the version of Tongo, she added.
She said the same applied to phone calls between Tongo and Mr Dewani.
"This telephone communication does not in itself corroborate what was said during those calls, it merely confirms that communication took place."
The prosecution had alleged the men carried out the killing for Mr Dewani for 15,000 rand (about £830).
The judge said Tongo and accomplices Mziwamadoda Qwabe and Xolile Mngeni were "intelligent men" and dismissed the prosecution claim that they would have carried out a contract killing for Mr Dewani for "a few thousand rand".Speaking outside court, South African National Prosecuting Authority spokesman Nathi Ncube said they were disappointed with the outcome but would respect the decision of the judge and not appeal.
"It is unfortunate that Mr Dewani has been acquitted because we believe that he was involved," Mr Ncube said.
"The court did not find that he was innocent, the court said it could not rely on the evidence given by three witnesses who themselves had been convicted of the crime."
Mr Ncube also denied that the case had collapsed because of a "shoddy police investigation".
He said: "The judgment centres around evidence that was given by three people. Nothing has been said about the police, nothing was said about how the prosecution could have done better.
"The fact of the matter is that we were relying on people who were themselves involved and implicated in the case."Tongo is serving an 18-year jail term for his role in the murder and Qwabe is part-way through a 25-year jail sentence for his role.
Mngeni was serving life for firing the shot that killed Mrs Dewani, but died in prison from a brain tumour.
The judge confirmed Monde Mbolombo, a self-confessed "link man", would no longer be granted immunity for his part in the plot.
The hotel receptionist admitted telling lies to the court to protect himself when the investigation first took hold. He had initially been granted immunity by prosecutors in return for being a state witness.
But the judge said: "As his evidence progressed, it became more and more clear of his involvement."
It will now be up to prosecutors to decide whether Mbolombo should face criminal proceedings.
