Lee, who received a suspended three-year prison sentence this year, was granted a special pardon to help the bid, Justice Minister Lee Kwi Nam , said in Seoul.
South Korea’s 2018 Pyeongchang Olympic Winter Games Bid Committee sought the pardon to help its chances of hosting the event at the third attempt.
Lee, an International Olympic Committee (IOC) member, said in 2008 he would refrain from acting in that capacity until his legal problems ended.
South Korean Presidents have a history of granting pardons to the leaders of its family-owned conglomerates called "chaebol", saying their value to the country outweighs the harm caused by white collar crime.
Lee, 67, ran Samsung for more than two decades helping transform Samsung Electronics Co. into the world’s largest makers of televisions, flat screens and memory chips, as well the second-largest producer of mobile phones.
Samsung is one of nine TOP partners sponsoring the Winter Olympics in Vancouver next year and London in 2012.
Civic groups, including the People’s Solidarity for Participatory Democracy, opposed the pardon because only four months had passed since Lee's sentencing.
Such a decision would be "very unfair" and hurt the principles of the constitution, the group said in a statement earlier this month.
Pyeongchang is making its third bid to host the Winter Olympics.
In 2007, the city lost to Russia’s Sochi for the 2014 Games, while in 2003 it was defeated by Vancouver.
South Korean prosecutors said in April 2008 that Lee also breached his fiduciary duty because he knew of illegal sales of bonds by Samsung Everland Inc., the group’s de facto holding company, and Samsung SDS Co. designed to transfer control of Samsung to his son, Lee Jae Yong .
In May, South Korea’s Supreme Court upheld a ruling that cleared the elder Lee of breach-of-duty charges related to Everland.
But, in August, the former chairman was found guilty of tax evasion and causing losses at SDS and was handed the sentence, suspended for five years but which also included a fine for 110 billion won (£58 million), allowing him to remain free.
A spokesman for the Government said: "The nation's business and sports circles have demanded a special pardon for former chairman Lee, citing the need to boost economic revitalisation and Pyeongchang's ongoing bid for the 2018 Winter Olympics."
November 2009: Calls growing for Lee to be given Presidential pardon to help Pyeongchang
November 2009: Pyeongchang 2018 want pardon for disgraced IOC member