The unification ministry, which must by law authorise cross-border contacts, said it has approved a request by the Eugene Bell Foundation, a US group which has a South Korean subsidiary, to send tuberculosis medicine to the North.
The aid is worth 336 million won ($305,177), a spokeswoman told AFP.
Seoul halted private cross border aid after the shelling killed four people including two civilians and sparked outrage in the South.
Thursday's approval followed a United Nations report last week which painted a dire picture of the humanitarian situation in the impoverished communist state.
"There have been voices that at least civic groups should be allowed to send aid to North Korea. The government has taken these factors into account," Yonhap news agency quoted a ministry official as saying.
The ministry would consider other requests by relief groups to send humanitarian aid, the unidentified official was quoted as saying.
The World Food Programme and other UN agencies said in their report last week that more than six million Northerners urgently need food assistance.
UN food agency officials visiting the South this week have stressed the need for major food aid for the North, without directly asking Seoul to contribute.
Tensions on the peninsula rose sharply after the shelling attack. But in an abrupt change of tack this year, the North has been calling for dialogue with the South and moderating its rhetoric.
It has also appealed to the United States and a variety of other countries for food aid.