"The military sincerely apologises to our people for causing worries over the incident," Col Lee Bung-woo, a spokesman at the Joint Chiefs of Staff (JCS), told reporters.
The military won't reprimand the two Marines, he said, noting they acted in line with engagement rules. Instead, the military will strengthen training for soldiers at guard posts to better distinguish civilian planes.
"The Marines don't deserve punishment because they didn't do anything wrong," Lee said.
"But we will map out ways to better educate soldiers of frontline units to prevent such incidents from happening again."
The two Marines guarding an island near the tense Yellow Sea border with the North fired their K-2 rifles at the Asiana Airlines plane flying in fog over the sea in a pre-dawn incident on Friday. The plane with 119 people on board was undamaged and no one was hurt, as the plane was flying out of range of the fire.
The incident illustrated high tensions on the Korean Peninsula, following North Korea's two deadly attacks on the South last year -- the sinking of the Cheonan warship and the bombardment of Yeonpyeong Island near the Yellow Sea border.
The two attacks killed 50 South Koreans, including two civilians. As a result, the South's military has vowed to take a tougher response than in the past if the North attacks again.