The suspects are leaders of Taksim Solidarity, an umbrella group at the forefront of the demonstrations.
They were accused of setting up a criminal group and violating public order and faced up to 30 years in jail.
Activist Mucella Yapici told AFP: "All of us were acquitted. It was an absurd case."
Human rights campaigners had demanded the charges be dropped, with Amnesty International calling it a "politically motivated show trial".
The protests began over plans to redevelop Istanbul's Gezi Park in May 2013, but turned into mass anti-government rallies after a heavy-handed police crackdown.
Mr Erdogan, who was prime minister at the time, said the demonstrations were the work of "riff-raff".
Hundreds of others are still being prosecuted across Turkey for alleged crimes related to the protests.
A Turkish court has acquitted 26 people charged over their role in organising protests against leader Recep Tayyip Erdogan in Istanbul in 2013.