This decision supports two previous judgments by lower courts, thereby clearing Mr. Jay Y. Lee from accounting fraud and stock manipulation allegations related to an $8 billion merger in 2015.
The Supreme Court's ruling has permanently removed a long-standing legal barrier for Mr. Lee, in the context of Samsung's efforts to catch up with the global race to develop advanced artificial intelligence (AI) chips.
The Supreme Court also upheld the appeal court's verdict, dismissing all allegations in the case related to a decade-long merger between Samsung's two subsidiaries, Samsung C&T and Cheil Industries.
Prosecutors said the merger was designed to strengthen Lee's control of the tech giant. A lower court also declared Lee innocent last year.
Samsung's lawyers said they are " Sincerely grateful" to the court for the decision, adding in a statement that the ruling confirmed the merger as legal. Samsung Electronics' stock changed after the verdict, up 1.7%.
Although the Supreme Court's ruling was widely predicted, it played a key role for Lee at this time.
He has faced many questions about his ability to lead Samsung Electronics - the world's leading manufacturer of memory chips and smartphones - as the company struggles with increasing competition and trying to catch up in the AI chip field.
For nearly a decade, Lee has faced legal challenges, including cases stemming from the merger that paved the way for his successor after his father, Lee Kun-hee, suffered a stroke in 2014 and fell into a coma.