The flight on Tuesday was part of a regular military surveillance exercise around a disputed, submerged, South Korean-controlled rock - known as Ieodo - that has long been a source of diplomatic tension with Beijing.
"We did not notify China," a defence ministry spokesman said.
China unilaterally declared a new "air defence identification zone" on Saturday over an area that includes Ieodo, as well as a set of islands at the centre of a tense territorial dispute between China and Japan.
The South Korean spokesman said military planes would continue to fly over the Ieodo area without providing any notification to China.