The court ruling comes as the two firms are locked in a bitter patent battle that could determine their fight for supremacy in the global smartphone market.
The Seoul Central District Court ruled that Apple breached two of Samsung's technology patents, and ordered it to pay 40 million won ($35 242) in damages, court officials said.
It also ordered Samsung to pay 25 million won for violating one of Apple's patents, Yonhap news agency said.
The court said the firms must halt sales of infringing products in South Korea, according to Dow Jones Newswires which said the banned products did not include the latest models of Samsung and Apple devices.
Samsung filed a lawsuit against Apple in Seoul in April 2011 regarding infringement of patents related to telecommunications standards.
Apple responded in June by filing a counter suit claiming Samsung copied the design and user interface of its iPhone and iPad.
The split ruling is not expected to make any impact on the broader dispute which involves legal action in several nations including the US and Australia.
The South Korean decision comes ahead of a high-stakes US jury verdict that is expected to signal the future course of the rival firms' tussle for smartphone supremacy.
In the US court, Apple is seeking more than $2.5bn after accusing the Korean firm of infringing designs and other patents. Samsung says Apple infringed its patents for wireless communication.
It is one of several legal cases around the world involving the two electronics giants in the hottest part of the tech sector - tablet computers and smartphones.
While the results so far have been mixed in courts in Europe and Australia, Samsung has a lot at stake in the US case, which could result in large damages or injunctions against its products in the American market.
A recent survey by research firm IDC showed Samsung extended its lead over Apple in the smartphone market in the second quarter despite slowing demand for mobile phones.
Samsung shipped 50.2 million smartphones globally in the April - June period, while Apple sold 26 million iPhones. IDC said Samsung held 32.6% of the market to 16.9% for Apple.
Samsung has steadfastly denied abusing Apple patents and countered in court that Apple has been taking advantage of some of the South Korean company's patented technology for wireless connections.