The bribery case is a retrial of an earlier one involving the country's former President Park Geun-hye, who was also jailed for bribery and corruption.
Lee has been the de facto head of Samsung Electronics since 2014.
The ruling is likely to have ramifications for the future of his role at the tech giant.
News of the sentence sent Samsung electronics shares more than 4% lower before they began to claw back some ground.
Lee's jail term will at least temporarily side-line him from decision making at the conglomerate.