Commander Omar Nizar, of Iraq's elite rapid response unit, had been sentenced to life imprisonment in June 2023 over the deaths of about 20 protesters and the injuring of 190 others on a bridge in the southern city of Nasiriyah in November 2019.
But the Court of Appeals has found there was "insufficient evidence" against Nizar.
The anti-government protests that began in October 2019 and mobilised tens of thousands of people for months were sparked by anger at decaying infrastructure, endemic corruption and youth unemployment, among other things.
A nationwide crackdown killed more than 600 people and wounded thousands more, with the repression particularly fierce in the poor and marginalised city of Nasiriyah.
Commander Nizar was jailed by a court for "giving the order... to fire live ammunition at the protesters on the Zeitoun bridge in Nasiriyah, causing deaths and injuries", the appeals court said.
The court, which gave its verdict last month, found there were substantial "doubts regarding the evidence against the accused Omar Nizar and the doubt must be interpreted in favour of the accused".
The ruling "annuls all the decisions made in the case and the accusation directed against the accused" and calls for "his release due to insufficient evidence", the verdict seen by AFP said.
It added that the plaintiffs were unable to provide "eyewitness testimony" against the accused and "their statements were contradictory" regarding his presence at the scene.
Nizar has been freed, an official told AFP on Wednesday.
The killings on the Zeitoun bridge, one of the bloodiest episodes of the protest movement, sparked outrage and eventually led to the resignation of then-prime minister Adel Abdel Mahdi.
In recent years, a small number of convictions have been handed down for the killing of activists and journalists during the protests.
In the summer of 2022, the United Nations mission in Iraq condemned what it said remained an "environment of fear and intimidation" that limits freedom of expression.
The UN was particularly critical of the "persistent impunity regarding targeted attacks against protesters... activists and dissidents holding critical views towards armed groups and the political actors affiliated with them".
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