Lee was first arrested in 2017 over allegations of political and corporate scandals linked to the then South African President Park Geun-hye.
With this, Lee will be sidelined from major decision-making at Samsung Electronics as it strives to overtake competitors, as well as from overseeing the process of inheritance from his father - who died last October - which is crucial to keeping control of Samsung.
Samsung was accused of paying 43bn won ($37.7m; £26.7m) to two non-profit foundations operated by Choi Soon-sil, a friend of Park's, in exchange for political support - alleged to include backing for a controversial Samsung merger which paved the way for Lee to become eventual head of the conglomerate.
The elder Lee died a year ago, leading to speculation that there would be a shake-up at Samsung as his heirs could be forced into asset sales or dividend payments to cover a massive inheritance tax bill.
Monday's sentencing can be appealed to the Supreme Court within seven days, the judge said, but legal experts said that because the Supreme Court has already ruled on it once, chances are lower that its legal interpretation will change.
Samsung Group is once again facing turmoil as its de facto chief, Lee Jae-yong, was again imprisoned in a bribery case, sparking worries that uncertainties may further increase over business and investment plans by the global tech behemoth in the post-pandemic era. In February 2017, the independent counsel concluded that Lee had offered bribes worth 29.8 billion won and promised to offer another 21.3 billion won to Park and Choi.
Lee's defence team expressed disappointment with the decision.
Lee assumed leadership of the company when his father Lee Kun-hee was hospitalised following a heart attack in 2014. With the lowered amount, Lee's sentence was slashed to a suspended jail term of two years and six months.
Lee will have to attend hearings in that case while serving his time in jail.
Two more former Samsung executives were imprisoned for two and a half years on similar charges. But he walked free after less than a year when an appeals court threw out some of the charges and suspended his sentence.
"The nature of the case is the former president's abuse of power, which infringed the business' freedom and property rights", said Lee In-jae, one of Lee's lawyers.
The company's shares fell nearly 3% on Monday, the day of the verdict against Lee, but regained most of that on Tuesday. It remains to be seen if Lee will appeal the ruling since the Supreme Court will likely uphold the latest high court decision. According to the Criminal Procedure Act, no appeal is allowed for a conviction of less than 10 years of prison term if it is meant only to reduce the sentence.