Chung Ho-young, the special prosecutor appointed by outgoing President Roh Moo-hyun, announced the result after a 40-day probe, Yonhap news agency said.
"The president-elect was not involved in the stock price manipulation," Chung Ho-young said, adding "we verified that Kim Gyeong-Jun was independently involved in stock manipulation using a paper company."
Lee Myung-bak strongly denied an involvement in the scandal for which his former business partner Kim Gyeong-Jun is on trial.
Lee is to take office on next Monday.