More than 30 people were injured when around 8,000 police broke up a blockade near the site by about 300 villagers and members of civic groups opposed to the THAAD installation.
Residents and activists have been terrified by reports of health hazards linked to THAAD and the possibility of being targeted in any North Korean attacks.
They had had attempted to block the road leading to the site on a disused golf course in the rural town of Seongju but were swept aside by riot police.
Several US military vehicles, including trucks carrying payloads covered in black sheets that appeared to be the launchers, then drove through.
Despite the violent demonstrations, the four remaining launchers of the system were fitted. Two launchers had already been deployed.
South Korean officials say THAAD will strengthen the country’s missile defences and will deter North Korea, which has missiles that can be fired from road-mobile launchers or submarines.
They also say the health fears are groundless and no such issues have been reported at other THAAD sites.
THAAD has also drawn strong objections from China, which believes the system’s radar could be used to pry into its territory and will upset the regional security balance.
Foreign Ministry spokesman Geng Shuang said: “We again urge South Korea and the United States to take seriously China’s and regional nations’ security interests and concerns, stop the relevant deployment progress, and remove the relevant equipment.”
China has agreed that the United Nations should take more action against North Korea after its latest nuclear test, while also pushing for dialogue to help resolve the standoff.
North Korea, which is pursuing its nuclear and missile programmes in defiance of international condemnation, said it would respond to any new UN sanctions and US pressure with “powerful counter measures” and accused the Washington of aiming for war.
The US wants the UN Security Council to impose an oil embargo on North Korea, ban its exports of textiles and the hiring of North Korean labourers abroad, and to subject leader Kim Jong-un to an asset freeze and travel ban.
Pressure from Washington has ratcheted up since North Korea conducted its sixth and largest nuclear test on Sunday.
The test, along with a series of missile launches, showed it was close to achieving its goal of developing a powerful nuclear weapon that could reach the US.