Bemba's supporters back in the DRC, meanwhile, celebrated the decision as a vindication.
Judge Christine Van den Wijngaert said Bemba, once the leader of Congo's main opposition party, could not be held responsible for crimes carried out by troops under his control in neighbouring Central African Republic in 2002-2003.
Bemba had appealed an 18-year sentence handed to him in June 2016 for crimes committed in the Central African Republic.
It added that the Trial Chamber made serious errors in its assessment of whether Mr. Bemba took all necessary and reasonable measures to prevent, repress or punish the commission by his subordinates of the other crimes within the scope of the case.
The former Congolese rebel leader was given 18 years in jail in what was hailed as a landmark ruling.
Solomon Sacco, head of Amnesty International's global justice team, said "the decision will be felt as a huge blow for the many victims of the "war against women" waged in the Central African Republic through a horrifying campaign of rape and sexual violence".More news: Fallout 76 will get mod support eventually
"We find it regrettable and troubling", Prosecutor Fatou Bensouda said.
"5229 survivors of Bemba's atrocities participated in the ICC proceedings - for these courageous individuals, as well as thousands of other victims in auto, the pursuit of truth, justice and reparations will continue".
"For these fearless individuals, as well as thousands of other victims in vehicle, the pursuit of truth, justice and reparations will continue", he added.
The conviction had marked several milestones.
"This was the first ICC case with a major focus on the use of rape as a weapon of war", she said. Bemba sent more than 1000 fighters to help stop the coup. He may not have murdered anyone with his own hands, but as the supreme commander of the Movement for the Liberation of Congo rebel forces, he is responsible for the crimes they committed.
However, appeal Judge Van den Wyngaert said the judges in the original case had "ignored significant testimonial evidence that Bemba's ability to investigate and punish crimes in vehicle was limited".More news: New Leaks For 2018 iPhone Suggest Triple Camera Module
Bemba has been in custody at the ICC for almost a decade after authorities in Belgium arrested him there in 2008 and sent him to The Hague.
CAR, meanwhile, has remained in an nearly constant state of turmoil.
There were scenes of jubilation never before witnessed inside the International Criminal Court.
"I cry with joy because Jean-Pierre Bemba was a dead man".
Some will say the verdict proves this court, often derided as a neo-colonial tool, is driven purely by truth and facts.
Amnesty International called the acquittal "a blow" to the victims.More news: Kim summit to cost Singapore 'around $20 million': PM Lee
Bemba was the highest ranking politician convicted by the permanent war crimes court, and his case had been seen as establishing a precedent that political and military officials may be held liable for the actions of troops under their command. But human rights organizations and the ICC's chief prosecutors provided enough evidence showing Bemba's guilt.
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