After a seven-week trial at Preston Crown Court, Duckenfield, a resident of Ferndown, Dorset, was found not guilty of all charges on Thursday.
Duckenfield had faced 95 charges of gross negligence manslaughter. There could be no prosecution over the death of the 96th victim, Tony Bland, due to the law at the time. Bland died more than a year and a day after his injuries were caused.
Men, women and children were crushed to death on the Leppings Lane terrace after a gate was opened to allow waiting fans to get into the stadium.
The jury of seven women and three men spent almost 14 hours in the jury room to consider their verdict. There were gasps in the courtroom when their not guilty verdict was announced, Xinhua reported.
The prosecution case was that Duckenfield had a personal responsibility for what happened at the match. He had ordered the opening of exit gates at the Leppings Lane end of the ground eight minutes before the match was due to start. The area outside the turnstiles has become dangerously overcrowded.
Barrister Benjamin Myers, who represented Duckenfield, maintained it was unfair that the retired cop should have become the focus of blame for the tragedy.
He told the court "We say that is unfair, there are so many other people at fault, and so many causes."
Just a few minutes into the start of the game the match was abandoned as attention turned to rescuing and helping injured fans.
Campaigner Margaret Aspinall, whose 18-year-old son James was among the 96, said "The question I'd like to ask all of you and people within the system is who put 96 people in their graves, who is accountable?"
The tragedy led directly to a change in the law forcing all top level football clubs in Britain to introduce all-seater stadiums. Until Hillsborough many fans preferred to stand on the terraces, in areas such as the famous Anfield Kop which had always been a standing area.
An everlasting flame burns at Liverpool's Anfield Stadium in memory of the victims of Hillsborough.
Families campaigned for years for an official hearing into the tragedy, leading to the prosecution of Duckenfield. In 2010 a Hillsborough Independent Panel was appointed to review previously unseen evidence. It led to new inquests being ordered into the deaths, opening in 2014 and lasting for two years, and becoming the longest inquests in British legal history.
In 2016 the inquest jury concluded the 96 who died were unlawfully killed. The jurors stated fans had played no part in the deaths and instead blamed police failures, stadium design faults, and a delayed response by the ambulance service.
In a statement Thursday night, Mike Benbow, a director at the Independent Office for Police Conduct (IOPC) said "We recognise today's verdict has huge significance for the families of the 96 victims of the Hillsborough disaster, its survivors, and the many thousands of people affected by the tragedy. As there are still live criminal proceedings relating to the disaster we will not be commenting further at this time."
Benbow warned people to avoid making any comments online that could prejudice any future legal proceedings.