The rockets were fired off the North's east coast and flew about 70km into the Sea of Japan, a ministry spokesman said.
"Following the North's rocket launch at 6:20pm (09:20 GMT), our military has maintained a close watch for possible North Korean provocations," the spokesman said Sunday.
South Korean troops have increased vigilance following a series of launches of rockets or missiles, AFP reported.
The activity coincides with annual South Korean-US military exercises that started in February and will run until mid-April.
Pyongyang routinely condemns such joint exercises as rehearsals for an invasion, while Seoul and Washington say they are purely defensive.