Lee, the first South Korean president-elect to undergo a criminal inquiry, was also cleared of owning land in southern Seoul under another person's name and lying about it, and of giving illicit business favours to a company while serving as Seoul's mayor from 2002-2006.
Rival politicians had pushed for the special investigation in an apparent attempt to keep the scandal alive throughout the vote.
Nevertheless, South Korean voters gave Lee a landslide victory in the December 19 election.
Lee said in comments released by his office: "It is fortunate that all suspicions were cleared once again.
"I thank the people who have given me trust and support so far. I think the way to repay this is to work harder and devote myself to serving the people and saving the nation's economy."
Even if Lee had been found at fault in the special inquiry, he would have been able to assume office on Monday as scheduled because the constitution grants sitting presidents immunity from criminal lawsuits unless they are accused of serious crimes such as treason.
However, it would have significantly undermined his authority.
The scandal came to a head in November with the extradition from the US of fugitive Korean-American fund manager Kim Kyung-jun, who once partnered with Lee to set up an internet financial firm.
Kim was accused of making millions of dollars by rigging stock prices from a separate investment company and fleeing to the US.
At issue have been allegations by Lee's liberal rivals that the money used for the stock manipulation came from a third investment firm, known as BBK, and that Lee was its real owner - meaning he was involved in the crime.
Lee has claimed the accusations were a plot by political rivals to discredit him.
Just days before the election, a 2000 video surfaced of Lee bragging that he had founded BBK, comments that Lee said were taken out of context.