Tokyo district judge Tamotsu Shoji stated that the Korean tech giant's products do not infringe upon Apple's patents concerning the synchronisation of media and data files between devices.
"We welcome the court's decision, which confirmed our long-held position that our products do not infringe on Apple's intellectual property," said Samsung in a statement issued to BBC News.
The Tokyo court's ruling follows Apple's landmark court victory over Samsung in the US, where the iPhone maker was awarded $1.05 billion (£665 million) in damages when a judge ruled that Samsung's Galaxy line infringed upon its software and design patents.
Apple has 30 days to appeal against the Japanese ruling, and has a host of other patent infringement lawsuits lined up against its competitor in the territory. The company is also pursuing legal action against Samsung in nine other countries.
Samsung previously confirmed that it will appeal against Apple's US victory.