In rejecting Apple's suit, Tokyo District Court Judge Tamotsu Shoji said Samsung's products did not infringe on the U.S. firm's technological scope.
A U.S. federal jury found last week that Apple did not infringe on any of Samsung's patents, while the South Korean firm had copied key features of iPhone.
The same jury awarded Apple $1.05 billion in damages and it is now seeking speedy bans on the sale of eight Samsung phones in the U.S. market.
"We welcome the court's decision, which confirmed our long-held position that our products do not infringe Apple's intellectual property," Samsung said in a statement following the verdict from the Tokyo court.
A representative for Apple in Japan declined to comment.
In Seoul, Samsung shares were up 0.7 percent in a flat market.
A spokesman for NTT Docomo Inc declined to comment, while a KDDI Corp spokeswoman said she did not see any major impact from the decision. Both Japanese mobile carriers sell the popular Samsung Galaxy series.
Shares in NTT Docomo last traded down 1.8 percent at a 2-week low, while KDDI was down 1.2 percent. Shares in local rival Softbank Corp <9984.T>, the first Japanese carrier to sell the iPhone and which doesn't sell the Samsung Galaxy line, were down 1.1 percent.
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