The former South Yorkshire Police chief superintendent had denied causing the deaths of 95 men, women and children in the disaster on 15 April 1989.
Mr Duckenfield, now 75, did not give evidence at his retrial at Preston Crown Court.
The seven women and three men who remained on the jury, following several discharges during proceedings, returned their verdict on Thursday following the six-week trial.
Gasps were heard from the public gallery as the foreman returned the verdict, while Mr Duckenfield sat impassive in front of the dock with his hands clasped.
One of the female jurors was in tears as the jury filed out of the courtroom.
Christine Burke, the daughter of victim Henry Burke who was killed in the tragedy, said the 96 had been found “unlawfully killed” by inquests.
Addressing the judge in tears following the verdict, she said: “I would like to know who is responsible for my father’s death because someone is.”
Margaret Aspinall, chair of the Hillsborough Family Support Group, said she blamed “a system that’s so morally wrong within this country, that it’s a disgrace to this nation”.
“Ninety-six are unlawfully killed and yet not one person is accountable” she added.
The Crown Prosecution Service confirmed that the acquittal marks the end of proceedings against Mr Duckenfield.
Families of the 96 victims had campaigned for 30 years over the crush, which unfolded during the FA Cup semi-final between Liverpool and Nottingham Forest.
Assistant Commissioner Rob Beckley, who led the investigation into Mr Duckenfield, said his thoughts were with survivors, the victims’ families and “the thousands of people who have been deeply affected by the events of 15 April 1989”.
“The jury had a difficult and challenging task examining evidence going back decades and I respect their decision,” he added.
“It may sound like a cliché to say ‘lessons must be learnt’, but today’s verdict means this has never been more relevant or important.
“It is right that an impartial and thorough investigation was carried out, and it is right that a jury was asked to make a judgement of the facts. What is wrong is that it has taken 30 years to get to this point.”
Mr Beckley said the 30-year delay between the disaster and trial had caused difficulties for everyone involved in the legal process.
“Thirty years means evidence has been corroded and some people and organisations cannot answer for their actions because they are no longer with us,” he added.
“Thirty years means myths took root about fans being a cause of the disaster, now unequivocally shown by both defence and prosecution evidence to be wrong. And 30 years means many people, especially families, have had to constantly relive their terrible experience.”
In 2016, investigators passed files on 12 individuals and three organisations involved in the disaster to the CPPS, but it only charged Mr Duckenfield and former Sheffield Wednesday club secretary Graham Mackrell.
The organisations referred were Sheffield Wednesday Football Club plc, the Football Association and South Yorkshire Metropolitan Ambulance Service.
Police said Sheffield Wednesday, which has been replaced by a new company, did not pass the CPS’s “public interest test” for prosecution.
A further seven individuals and two organisation suspected by Operation Resolve of committing an offence were not referred – three of the suspects had died since the disaster and there was insufficient evidence on the other individuals.
Structural engineering firm Eastwood and Partners, which the trial heard wrongly calculated the capacity of the terrace, was not charged as it no longer exists as it did in 1989.
The CPS advised that Sheffield City Council could not be prosecuted under the Safety of Sports Grounds Act because it was the regulating authority and issuer of the safety certificate and therefore could not be subject to offences under the same law.
The criminal investigation into the Hillsborough disaster cost almost £60m after being set up in 2012, seeing up to 200 investigators sifting through 143,000 documents, pieces of footage, and evidence.
The court heard how Mr Duckenfield had ordered the opening of exit gates at the Leppings Lane end of Hillsborough stadium at 2.52pm, eight minutes before kick-off.
He was responding to calls from other police officers after the area outside the turnstiles became dangerously overcrowded as Liverpool fans tried to enter the stadium.
Exit gate C was opened, causing 2,000 fans to quickly enter, with many heading for a tunnel straight ahead that led to the central pens where the crush happened.
Witness statements heard at the trial described trapped people screaming for help and to be let out, but police did not open gates at the front of the pens that eased a previous crush.
Mr Duckenfield did not give evidence in the trial as the court heard he was suffering from post-traumatic stress disorder.
Judge Sir Peter Openshaw also told jurors the condition could explain Mr Duckenfield’s lack of reaction as he sat in the well of the court throughout the trial.
He said: “He has a resilient, passive and expressionless external presentation which gives no indication of his state of mind so don’t draw an adverse inference against him.”
The court was played audio of the retired chief superintendent giving evidence to inquests in 2015.
In those hearings, he accepted he should have taken steps to close the tunnel to the central pens after ordering the opening of the exit gate.
Sir Peter had told jurors that they had to answer five questions when deciding their verdicts, including whether Mr Duckenfield had caused an obvious risk of death by crushing.
He added: “For negligence to be found to be ‘gross’, it must be: having regard to the foreseeable risk of death; so truly and exceptionally bad; so blameworthy; so reprehensible; and so deserving of punishment, that it deserves to be marked by conviction of the serious crime of manslaughter.”
The first jury to consider the case, which initially went to trial in January, failed to reach a verdict on charges against Mr Duckenfield in April.
The victims were Liverpool fans who had flowed down a tunnel at the Leppings Lane end of the ground into overcrowded pens.
The law did not allow prosecution over the death of the 96th victim, Tony Bland, as he died more than a year and a day after his injuries were caused.
Additional reporting by PA
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