Won, 64, was convicted in September last year of illegally engaging in political acts as head of the National Intelligence Service (NIS).
The charges related to an online smear campaign by NIS agents against the opposition party candidate whom the current president, Park Geun-Hye, defeated in the 2012 poll by a narrow margin.
A district court initially gave Won a two-and-a-half year suspended sentence, ruling that while there was clear evidence of wrongdoing, there was not enough proof that he had directly sought to influence the outcome of the ballot.
In its unanimous decision today, the Supreme Court declined to rule on Won's guilt, but ordered the High Court to re-examine what it described as deficient evidence regarding crucial e-mails and tweets.
More From This Section
"The court ... Returns the case for further review," said Chief Justice Yang Sung-Tae.
The decision did not release Won from custody, but his defence team said they would file a bail request with the High Court.
"The Supreme Court avoided handing down a verdict, while demanding further fact-finding efforts at the appeals court," said Won's lawyer Lee Dong-Myong.
"To put it simply, the court says this case has not matured enough to move from fact-finding procedures to the stage of handing down a verdict," he added.
The spy agency, which has changed titles over the years, had a particularly notorious reputation in the decades of authoritarian rule before South Korea embraced democracy in the 1980s.
The modern-day NIS has been tainted by a series of scandals, including the forging of documents to build a false spying case against a former Seoul city official who had escaped to South Korea from the North in 2004.
Briefing legislators yesterday, NIS officials admitted purchasing a hacking program from an Italian company but denied using it to monitor South Koreans.
The intention was to boost the country's cyber warfare capabilities against North Korea, the officials said.