The court overturned the verdict on "procedural grounds", the state-run Anatolia news agency reported, without elaborating.
The development opens the way for a retrial of eight suspects including four police officers accused of taking part in the killing of Ali Ismail Korkmaz, 19, in June 2013.
Last year, a lower court sentenced Mevlut Saldogan to 10 years and 10 months in prison and fellow police officer Yalcin Akbulut to 10 years for the killing in the western city of Eskisehir.
Korkmaz died after being pummelled with baseball bats and truncheons in one of the most notorious examples of police brutality in the protests against the government of President Recep Tayyip Erdogan, who was then prime minister.
The teenager suffered a brain haemorrhage and died after 38 days in a coma.
He was one of eight people killed in the three weeks of unrest sparked by plans to redevelop an Istanbul park that grew into a nationwide wave of anger against Erdogan.
The family of the victim and his lawyers had denounced the sentences as absurdly lenient. Prosecutors had demanded life in prison.
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