The two North Korean boats, which normally serve to keep fishing boats on the right side of the boundary, crossed "one nautical mile south" into South Korean waters, a defence ministry official told AFP.
The pre-dawn incursion prompted a South Korean naval ship to fire several warning rounds, after which the two vessels retreated to the North side of the border.
The official said the patrol boats might have been chasing some Chinese crabbing boats fishing illegally in the area.
"Or the North might have wanted to check the South's military vigilance," he added.
The North does not officially recognise the Yellow Sea boundary, which was unilaterally drawn by the US-led United Nations forces after the 1950-53 Korean War.
The border has been the scene of brief but bloody naval clashes in 1999, 2002 and 2009.
The Korean conflict ended in an armistice instead of a peace treaty and technically the two Koreas are still at war.
It is not rare for North Korean patrol boats and fishing boats to cross the unmarked sea border into the South, but the timing was sensitive Friday with Obama's arrival.
Tensions are high on the Korean peninsula, with multiple indications that North Korea might be planning to carry out a fourth nuclear test.
North Korea has conducted three tests in 2006, 2009 and 2013.
