It's another escalation of tension between the rivals that prompted the South respond with live fire drills.
The exchange led residents of two remote South Korean islands on the western maritime frontier to evacuate to bomb shelters at the instruction of the South's military, before it fired live rounds towards the disputed Northern Limit Line (NLL) border.
The firing by North Korea caused no civilian or military damage in the South, said South Korean military spokesperson Colonel Lee Sung Jun.
"We sternly warn North Korea that they are fully responsible for this escalation of the crisis, and we strongly urge them to stop it. Our military is tracking and monitoring related situation in close cooperation with the U.S. and South Korea, and will implement measures in response to North Korea's provocations."
China, which is North Korea's main political ally, urged restraint and called on the two sides to resume dialogue.
Yeonpyeong is home to just over 2,000 residents and troops stationed there, about 75 miles west of Seoul and accessed by ferries that take more than 2-1/2 hours.
Residents of Baengnyeong island which lies far to the west of Yeonpyeong and also near the sea border, were also told to seek shelter. Its population is about 4,900.
The escalations have left South Koreans in Seoul fearing conflict between the neighbors could resume.
"I served on Baengnyeongdo Island until last month, so I know that North Korea's provocation at any time is not strange at all. After hearing the news, I feel worried and am kind of afraid that war can occur."
North Korea has warned in recent days that the situation on the Korean peninsula is spiralling towards war because of dangerous moves by the U.S. and South Korean militaries.
Both Koreas have vowed crushing military responses if attacked.
