Of 300 lawmakers of the unicameral National Assembly attending the historical plenary session, 204 voted in favor and 85 against with three abstentions and eight voided, Xinhua reports.
The first impeachment motion was confirmed invalid last Saturday after most of the 108 ruling People Power Party left the parliamentary hall and refused to cast ballots.
With the parliamentary approval, the constitutional court will deliberate the impeachment for up to 180 days, during which Yoon's constitutional power will be suspended and Prime Minister Han Duck-soo will be an acting president.
If the impeachment is upheld by the court, a snap presidential election would be held within 60 days.
It marked the third presidential impeachment in the Asian country's modern history. Former conservative President Park Geun-hye was removed from office by the constitutional court in March 2017.
Late liberal President Roh Moo-hyun was impeached by the National Assembly in March 2004, but the constitutional court restored Roh to power about two months later.
Yoon declared an emergency martial law on the night of Dec. 3, but it was revoked by the National Assembly hours later.
The president said in an address to the nation on Thursday that his martial law imposition was an act of governance to protect against the "legislative dictatorship" of the majority opposition.
The main liberal opposition Democratic Party and five other minor parties, which proposed the impeachment motion earlier this week, believed that Yoon's martial law declaration was illegal and unconstitutional.
According to the motion, the martial law can be imposed only when the country faces "state of war, serious incident or other comparable national emergency" that lead to engagement with the enemy or extreme disturbance of social order.
The opposition noted that no sign of national emergency was detected at the time of Yoon's declaration, denouncing Yoon for failing to follow procedures for a martial law imposition, such as an immediate notification to the National Assembly.
Calling Yoon the "ringleader" of mutiny, the opposition said in the motion that Yoon committed treason by declaring the martial law and mobilizing the military and police to prevent the National Assembly from rescinding the martial law order.
According to a survey of 1,005 voters conducted Tuesday by a local pollster Embrain Public, 78 percent were in favor of Yoon's impeachment, while 20 percent were against it.
Those who replied that Yoon committed rebellion, punishable by up to death, reached 69 percent, while 68 percent said Yoon should immediately be arrested.
Read the full news report by Xinhua here!