Lee "was immediately arrested in court to be sent to jail", the Financial Times reported.
Lee's violations came during his time as Samsung chief financial officer between 2012 and 2017; he has been chairman of the board since March 2018.
Samsung VP Kang Kyung-hoon also received an 18-month prison sentence for his involvement, the Financial Times wrote.
The sentences were handed down by the Seoul Central District Court. In all, about 25 current and former Samsung executives were found guilty on similar charges of violating labour laws.
"The case largely focused on efforts by Samsung officials, including Lee, to dismantle the labour union at the company's customer-service unit."
The court convicted Samsung officials on multiple charges, including gathering personal information on some union members, such as their marital status, personal finances, and mental health histories.
Samsung said that the company's "understanding and view towards labour unions in the past fell short of society's expectations".
As Samsung board chairman, Lee Sang-hoon "is responsible for convening quarterly board meetings and reviewing the company's financial statements before they are sent to shareholders for a vote, among other responsibilities", the FT wrote.