According to South Korean media, between 60 to 70 homes caught fire when the shelling started, and civilians fled for shelter.
The island, which is along the disputed sea border of the two countries, houses military installations, and about 1,500 civilians. Most are fishermen.
The clash started when South Korea began carrying out annual military drills in disputed waters. North Korea protested and warned the South to stop or face retaliation.
It was the heaviest attack in the region since the Korean War 60 years ago. North Korea reportedly targeted the most populated part of the island.
South Korea returned fire and dispatched fighter jets in response, and said there could be considerable North Korean casualties as troops unleashed intense retaliatory fire. The supreme military command in Pyongyang threatened more strikes if the South crossed their maritime border by "even 0.001 millimeter," according to the North's official Korean Central News Agency.
South Korea has upgraded its military posture to its highest non-wartime alert.
"The firing of artillery by North Korea against Yeonpyeong Island constitutes an indisputable armed provocation against the Republic of Korea," said South Korea's Blue House [the equivalent of the U.S. White House] in a statement. "It even indiscriminately fired against civilians. Such actions will never be tolerated."
Government officials in Seoul called the bombardments "inhumane atrocities" that violated the 1953 armistice halting the Korean War. The two sides technically remain at war because a peace treaty was never signed.
The U.S. has tens of thousands of troops currently in South Korea.
Obama was awoken by his national security advisor at 3:55 a.m. Eastern Time to brief him on the situation. The U.S. is condemning the attack, but Stephen Bosworth, the U.S. special envoy to North Korea, emphasized that military action would be a last resort.
"We strongly believe that a multilateral, diplomatic approach is the only way to realistically resolve these problems. We are very committed to continue to work at that in every way possible," Bosworth said.
The attack occurred just days after three Stanford University scientists returned from visiting a North Korean nuclear facility. The scientists determined that the North's nuclear program was far more advanced than anyone had expected.
The Pentagon has not moved any additional troops to the Korean peninsula, and Obama is also tempering his direct involvement.
The Associated Press contributed to this story.