Europe's anti-trust regulator launched an investigation earlier this year into whether Samsung was failing to license those patents under fair and reasonable terms.
In Friday's ruling, the South Korean court said Samsung did not abuse its market power as an industry standard patent holder.
Apple filed suit against Samsung in San Diego, California, in April 2011, alleging that some of the South Korean company's smartphones and computer tablets are illegal knockoffs of Apple's iPhone and iPad. Samsung denies the allegations and argues that all companies in the cutthroat phone industry mimic each other's successes without crossing the legal line.
Cupertino, California-based Apple is suing Samsung for $2.5 billion and demanding that the court pull its most popular smartphones and computer tablets from the U.S. market, making the case one of the biggest technology disputes in history.
Jury deliberations in San Diego began Wednesday after three weeks of testimony. The case went to the jury after last-minute talks between the companies' chief executives failed to resolve the dispute.
Shortly after Apple filed its suit in the U.S., Samsung filed a complaint in South Korea against Apple for allegedly breaching its telecommunications patents.
The battle is all the more complex as Apple and Samsung are not only competitors in the fast-growing global market for smartphones and tablet computers, but also have a close business relationship.
"This is going to go on and on and on," said Barney Loehnis, head of mobile for Asia at public relations firm Ogilvy. "This will never change because the sorts of patents that they're fighting over are such a fundamental essence of using these devices that they're always going to be leapfrogging one over the other."
Samsung, the world's biggest manufacturer of memory chips and liquid crystal displays, supplies some of the key components that go into Apple products, including mobile chips that work as a brain of the iPhone and the iPad.
The South Korean firm overtook Apple in less than three years in smartphone markets. In the second quarter of this year, Samsung sold 50.2 million units of smartphones, nearly twice as much as Apple's 26 million units, according to IDC.
Despite the ruling that is widely seen as Samsung's victory, Samsung's share fell 0.9 percent in Seoul.
AP business writer Kelvin Chan in Hong Kong contributed to this report.
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