Seoul prosecutors earlier charged the 73-year-old journalist with "distributing" materials that praised the communist North by following Pyongyang's official Twitter account, @uriminzok.
Lee was, however, found guilty of supporting the North in his own blog postings and was sentenced to a one-year jail term, suspended for two years.
South Korea's National Security Laws, enacted in 1948 to protect the fledgling state from infiltration by the communist North, ban its citizens from praising or sympathising with Pyongyang.
The Seoul Western District Court ruled that, because Lee only followed North Korea on Twitter and did not re-tweet or mention any of the posts on his own account, he had not broken the law.
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"It can't be said that he 'distributed' those posts as they were only shown on Lee's own account and were not shown to other people, such as Lee's followers," the court said in a statement.
Its Twitter account has over 18,500 followers.