The former Seoul mayor and business tycoon secured a landslide victory in last month's presidential election and promised to revive the country's economy.
Lee is the first South Korean president-elect to face a criminal investigation.
'Rigging stock prices'
Prosecutors cleared Lee after they could not find any evidence that he conspired with
a Korean-American fund manager in 2001 to manipulate stock prices.
The case was re-opened after a video clip widely circulated on the internet purportedly showed Lee admitting to establishing the fraud-ridden asset management company.
Kim Kyung Joon, the head of the controversial investment firm BBK, and Lee's business associate in a previous venture, was indicted on December 5 on charges of rigging share prices and embezzling tens of millions of dollars from the company.