Jubilant activists praised the decision which they said was a defence of democratic freedoms at a time when Beijing is ramping up pressure on the self-ruling island.
China sees Taiwan as part of its territory and is pushing for reunification, with Beijing signalling a harder line towards what it regards as a renegade province.
Thousands of people took to the streets in protest in March 2014 in what became known as the Sunflower Movement, with 200 people occupying the main chamber of parliament for three weeks.
"The defendants did not initiate attacks or cause bloody conflicts and it was an expression of democracy," judge Chang Huei-li told the court as she upheld last year's acquittal by a lower court.
She said protesters were reacting to flaws in the legislative process and the failure of lawmakers to reflect public opinion.
"Those who have power should listen to people's voices and promote their welfare," Chang said.
Taipei's district court had ruled the protesters' actions reflected their right to civil disobedience, clearing them on charges of incitement and interfering with public functions.
Protest leader Huang Kuo-chang, now a lawmaker, said Tuesday's judgement reaffirmed Taiwan's freedoms.
"When lawmakers do not carry out their duties properly the people can stand up and resist and their rights are protected," Huang said after the ruling.
Sunflower leader Chen Wei-ting said Taiwan's transparent legal process was a message to China's President Xi Jinping, who was granted a lifetime mandate as leader Sunday.
"I want to tell Xi Jinping that even if you can become an 'emperor' and have endless terms, Taiwan is a democratic country," said Chen.
"I hope our friends in Hong Kong who are in a difficult situation will not give up. Taiwan will alway stand with you," Chen said after the hearing.
Fears over warming cross-strait ties contributed to the plummeting popularity of Ma Ying-jeou's Kuomintang government and its defeat in the 2016 presidential elections at the hands of the Democratic Progressive Party (DPP).
Relations have since turned rapidly frosty as Beijing-sceptic President Tsai Ing-wen refuses to acknowledge the island is part of "one China".
A court spokesman said Tuesday's acquittals were final.
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