The North Korean soldiers retreated after the warning shots were fired on Thursday morning.
They had breached the Military Demarcation Line running through the middle of the Demilitarised Zone about 11am.
It is at least the third such incident this month. South Korea's military fired warning shots on Tuesday after dozens of North Korean soldiers breached the demarcation line.
Although deadly clashes have occasionally occurred over the decades since open fighting between the countries stopped at the end of the 1950-53 Korean War, the recent incidents mark a rare uptick in activity close to the demarcation line.
The incident came after Russian President Vladimir Putin visited Pyongyang for the first time in 24 years this week.
Kim Yo-jong, the powerful sister of the North's leader, separately issued a statement on Friday denouncing South Korean activists who late on Thursday flew balloons carrying leaflets towards the North, saying they will soon be criticised by their own people.
The launching of the balloons has been a source of rising tension between the two Koreas, as the North flew its own - carrying trash - to the South, causing some property damage.Â
Seoul retaliated by resuming border loudspeaker broadcasts.
Kim did not say how the North might respond but the mention of the criticism within South Korea against the balloon launches most likely referred to the demands by some residents near the border that such activities be halted over safety concerns.
She made no mention of the incident involving the troops.
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