Washington and Seoul agreed to deploy a Terminal High-Altitude Area Defense system, known as THAAD, in a mountainous region southeast of Seoul to counter a growing missile threat from North Korea.
The submarine launch came shortly after the original announcement of South Korea's THAAD defense system and the US placing even stricter sanctions on North Korean leader Kim Jong Un for alleged human rights abuses.
North Korea fired three ballistic missiles that flew between 500 km and 600 km (300-360 miles) into the sea off its east coast, South Korea's military said, the latest in a series of provocative moves by the isolated country.
The Seoul government has persistently said that it has no intention of joining the MD system and that it wants to build up its own "Korea Air and Missile Defense" system to deal with evolving North Korean missile and nuclear threats.
North Korea is believed to be developing nuclear warheads and trying to miniaturise them to mount on ballistic missiles but it is believed by experts to be a few years away from mastering the technology.
Conflict between North Korea and South Korea dates back to 1950, after Korea was liberated from Japan and the cold war split the nation between Russian supported North Korea and United States supported South Korea.
Korea's defense minister said Wednesday that the planned deployment of an advanced US anti-missile system is for self-defense and will not be incorporated into the wider USA missile defense system.
North Korea's official media reports did not say when the tests took place, but they were most likely referring to the country's test-firing Tuesday of three ballistic missiles - two short-range Scuds and one medium-range Rodong.
The US, Japan and Seoul have condemned the exercise. "Such actions are not conducive to reducing tensions on the Korean Peninsula." said Farhan Haq, a spokesman for UN Secretary General Ban Ki-moon.
The Korean People's Army (KPA) said in a statement that the US military forces in South Korea will be the first targets of any attack, followed by South Korean "puppet" troops.
The resolution passed in early March is in response to North Korea's earlier nuclear and long-range missile tests.
Lee Chun-geun, a scientist at South Korea's Science and Technology Policy Institute, said the North Korean missiles were believed to be carrying warheads, which contain trigger devices but not plutonium or uranium, to see whether those warheads could detonate properly.