Lee and about 25 other defendants were convicted of violating labor union-related laws.
Prosecutors said Samsung executives had used several tactics to target union activities, including closing sub-contracted firms with active unions.
Samsung has not yet commented on the ruling.
Seoul Central District Court said plans to stop union activities had been masterminded by executives in the firm's now-defunct elite strategy group.
The case on Tuesday focused largely on efforts by officials to undermine union activities at the customer service unit when Lee was serving as chief financial officer.
Other tactics used by the defendants to target unions included finding out sensitive information about union members to convince them to leave, and delaying negotiations between labor unions and management, prosecutors said.
The jury said there were "countless documents" detailing tactics to undermine union activities that were distributed to affiliates by the elite unit.
"While Lee claims there were many areas he did not know much about, [we] cannot give him immunity only due to the fact that [he] was not aware of the peripheral areas," the judge said, according to Yonhap news agency.
The extent and details of the charges against the defendants found guilty on Tuesday varied.
The verdict followed a ruling last week that saw Samsung Electronics Vice-President Kang Kyung-hoon sentenced to 16 months in prison on charges of union-busting.
Park Sang-in, a professor at Seoul National University, told Reuters news agency that Tuesday's ruling marked "a further signal of change for the South Korean judicial system, which previously gave lenient sentences to convicted businessmen."
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