Kaneko, who was a research assistant at Tokyo University until his arrest in 2004, was ordered to pay a 1.5-million-yen (13,000-dollar) fine in Japan's first ruling on file-sharing software.
But the Kyoto District Court turned down a call from prosecutors for a one-year prison sentence for Kaneko, who pleaded not guilty.
Judge Makoto Himuro said in the ruling that Kaneko "had realized the software would be widely used in its form to violate copyrights."
The judge said nearly 90 percent of files swapped by Winny are illegally copied.
But he also showed leniency toward the programmer and said the defendant "had seen the necessity and possibility to construct a new business model as an engineer."
Kaneko, who is said to have designed his first computer program while in elementary school, has become a cause celebre for Japanese Internet buffs.
He is known in cyberspace as "47" -- a reference to his posting on a message board declaring Winny's creation -- and has amassed thousands of dollars in donations for his legal defense.
Winny, which can be obtained for free on the Internet, is reportedly still used by up to 450,000 computers in Japan.
It allows the anonymous exchange of files, facilitating the transfer of music and movie files and obscene content.
But Winny has also been said to suffer programming flaws as it has been the source of a series of information leaks, including from a number of computers belonging to government and company officials who used the software privately.
Prosecutors had argued that Kaneko intended to destroy the system of copyright protection by inventing and releasing the software.
The defense counsel countered that the programmer should not be responsible for the illegal acts committed by Winny's users.