The International Criminal Tribunal for Rwanda convicted Ndindiliyimana in 2011 of genocide, murder and other serious violations of international law for his role in atrocities in Rwanda in 1994.
The appeals chambers said Tuesday it reversed the conviction against the former paramilitary general, who's been in custody for the better part of the decade, saying the prosecution conceded on appeal that nothing supported the conviction.
"Consequently, Ndindiliyimana, who had been sentenced to time served by the trial chamber, was acquitted of all counts in the indictment," the court said in a statement.
Maj. Francois-Xavier Nzuwonemeye was acquitted after the court found the prosecution erred in holding him responsible for certain war crimes.
His subordinate, Capt. Innocent Sagahutu, had his jail term reduced by five years to 15 years. He was found guilty of aiding and abetting in the slaying of Belgian peacekeepers but the court reversed a decision saying he ordered the killings.
"The appeals chamber also found that the trial chamber committed errors of law and fact and concluded that neither Nzuwonemeye nor Sagahutu could be held criminally responsible for the killing of Prime Minister Agathe Uwilingiyimana [in 1994]."
At least 800,000 people were killed during the Rwandan genocide over the course of 100 days in 1994.