The anti-missile system, Terminal High Altitude Area Defence System, known as THAAD, has been put in place despite opposition from activists and China.
THAAD is designed to shoot enemy missiles out of the sky without detonating any warheads attached to them.
The Delta Battery, 2nd Air Defence Artillery Regiment from Fort Bliss in Texas was deployed to South Korea in April to begin moving the system into place.
The overnight operation occurred nearly a year after Washington and Seoul agreed to position the battery in a remote southeastern area to counter the growing threat from North Korea.
The Delta Battery was officially realigned with the 35th Air Defence Artillery (ADA) Brigade from the 11th ADA Brigade on Thursday in a reflagging ceremony in THAAD’s new home in Seongju.
A statement from the 35th ADA public affairs office said: “The transfer of authority allowed D-2 to redeploy stateside to prepare for the unit’s return to South Korea on permanent change of station orders.”
An army statement said: “The 35th ADA Brigade now employs the full complement of the U.S. Army’s ADA capabilities in the Republic of Korea, consisting of Avenger, Patriot and THAAD.”
Earlier this month US Forces Korea (USFK) announced the deployment of the Terminal High Altitude Area Defence (THAAD) system is a “tentative” attempt to foil any spontaneous plots from despot leader Kim Jong-un.
The USFK said: “THAAD intercepts short and medium range ballistic missiles inside and outside the atmosphere.
“It is interoperable with other ballistic missile defence systems, highly mobile, and deployable worldwide.”
The system, that was announced last month, can identify incoming missiles “at ranges up to 1,000 km [621miles]”.
The range of the THAAD system allows North Korea and some parts of China to be scoured for potential threats.
Beijing has voiced intense opposition to the radar technology due to a spying risk.
However, military experts have attempted to extinguish China’s complaints by stating that the optimal range of the system is 372miles (600km) to 497 miles (800km).
The installation of the THAAD system comes as the region seems to be poised to descend into could be World War 3.
After several missile tests by North Korea’s leader Kim Jong-un and an increasingly hostile war of words with US President Donald Trump the situation has deteriorated rapidly.
As well, North Korea has entered into a war of words with most of its neighbours, most notably Japan.
The rogue state, which has fired two rockets over Japanese territory this year, sent the warning “you will pay for your crimes”.
Pyongyang-based newspaper issued the threat to Tokyo which was a reference to past government-general rule over Korea enforced by Japan.
North Korea officials also vowed to make “nuclear clouds” over Japan.
Korean Central News Agency said the behaviour of Japan in calling for international “maximum pressure” on the rogue state was “little short of mad”.
The statement read: “Inciting tensions on the Korean peninsula is a suicidal deed that will bring clouds to the Japanese archipelago.”
Former US President Jimmy Carter said he would be willing to travel to North Korea on behalf of the Trump administration to help diffuse rising tensions, The New York Times reported on its website on Sunday.
Mr Carter, 93, said: ”I would go, yes,” when he was asked in an interview at his ranch house in Plains, Georgia whether it was time for another diplomatic mission and whether he would do so for President Trump.