The rallies three years ago, which saw thousands take to the streets and some 200 people occupy parliament for weeks, expressed growing anti-China public sentiment and contributed to the plummeting popularity of Taiwan's former Beijing-friendly Kuomintang government.
Taiwan, now under a Beijing-sceptic leadership, has been self-ruling since splitting from the mainland in 1949 after a civil war -- but it has never formally declared independence and China still sees it as part of its territory.
Prosecutors charged Huang Kuo-chang -- an academic who was a key face of the movement and has since joined parliament -- with incitement and interfering with public functions in 2015, along with 21 others.
But Taipei District Court found them not guilty Friday, saying their actions were justified out of interest for the public.
"Expressing their political views on public affairs is in line with the social interest," the court said in a statement.
Huang is now chairman of the pro-independence New Power Party (NPP) founded after the protests, which is now the third-largest in the legislature after winning five seats in elections last year that toppled the Kuomintang (KMT) from power.
Protesters in the Sunflower Movement complained that the KMT had agreed to a trade deal in secret that would leave export-reliant Taiwan vulnerable to Chinese influence.
Days after taking office in May last year, the new Democratic Progressive Party (DPP) government dropped a separate lawsuit against Sunflower protesters for infiltrating the cabinet headquarters.
Premier Lin Chuan said at the time the movement has "legitimacy and social contribution".
Cross-strait ties have deteriorated since President Tsai Ing-wen came to power with all official communications cut off, ending an eight-year rapprochement.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)