The Koreans were released unconditionally Saturday, two days after Rep. Lee Sang-deuk met with Libyan leader Moammar Gadhafi, Yonhap News Agency reported. Lee is the older brother of President Lee Myung-bak.
The men, identified only by their family names of Koo and Jeon, were handed over to their families, the ministry said.
Korean officials had earlier expected the two would be tried and deported after sentencing. They were arrested in the summer, accused of Christian missionary work.
The release came as Lee's visit ended a long diplomatic standoff after Libya accused a South Korean of spying for Seoul. Tripoli charged the person, whom it expelled, gathered information about Gadhafi and weapons systems and passed it to the United States and Israel.
Libya then shut down its economic cooperation bureau in Seoul, its de facto embassy, and sent staff who worked there to China.
A South Korean diplomatic source said Seoul will recall Ambassador Chang Dong-hee from his post as a reprimand to Libya.