The approval, which paves the way for the tariff-slashing accord to take effect as early as July, came in a one-sided late night vote Wednesday that saw Grand National Party lawmakers wield their majority in the National Assembly. EU lawmakers approved the deal earlier this year.
The free trade agreement brings together increasingly affluent South Korea, Asia's fourth-largest economy, with the 27-member EU, the world's largest economic bloc. Trade between the two sides totaled $92.2 billion last year, a gain of 17 percent from the year before. It is the EU's first such accord with an Asian country.
A total of 169 National Assembly members were present and 163 voted in favor of the legislation, which passed a little more than an hour before midnight. One lawmaker voted against it while five abstained. The assembly has 299 members.
"I announce that the free trade agreement between the Republic of Korea and the European Union has been ratified," National Assembly Speaker Park Hee-tae said after the vote.
The main opposition Democratic Party boycotted the session in a dispute about providing safeguards for farmers and small retailers, Yonhap news agency reported.
Members of the smaller Democratic Labor Party protested by standing near the speaker's chair and holding up signs reading "Oppose the Korea-EU FTA" after Park ended debate ahead of the vote.
Negotiations toward an agreement began four years ago soon after South Korea and the United States concluded negotiations on a free trade deal. Despite the later start, Seoul and Brussels stand to see their accord take effect first - a potential development that has worried U.S. businesses who see European rivals potentially gaining an advantage in the South Korean market.
The EU ranks as South Korea's fourth-largest trading partner behind China, the Association of Southeast Asian Nations and Japan. The U.S. is South Korea's fifth-largest trading partner.