The students attacked American troops at the Yongsan Base in the latest violent explosion of anger since the girls were crushed to death by an armoured vehicle taking part in a training mission.
The United States Forces Korea (USFK) said three US Army staff at the main base in Seoul were kicked and beaten by the protesters before they could be contained.
The students were then escorted off the base by South Korean police, the USFK said. Seventeen were detained.
Anti-US activists have rejected as insincere a series of official US apologies for the accident, which took place in a rural area north of Seoul.
South Korean political groups, and North Korea, have seized upon the accident to press for a US troop withdrawal.
The US embassy has been attacked and there have been other peaceful demonstrations against the continued US presence.
'Yankee go home'
In the latest incident, the students ran 50 metres inside the army headquarters before scuffling with US military and South Korean civilian police.
They shouted "Yankee go home", demanding the withdrawal of the 37,000 US troops stationed in South Korea.
They also wanted the two soldiers involved in the accident be sent to a South Korean civilian court, as requested by the country's government.
South Korean police said the protests were soon stopped and the students were removed from the base in under 10 minutes.
Colonel Peter Champagne, the military police commander, issued a statement saying that the intrusion was quelled quickly by officers.
"This was a difficult situation because they were being kicked and physically assaulted by many of the trespassers," he said.
Medical treatment
A spokeswoman for the US military command, Lee Ferguson, said two American military policemen and an Army lieutenant were "kicked and pummeled" by the protesters but were not seriously injured.
"The injuries were mostly bruising, and none of them was hospitalised," she said.
One student was sent for medical treatment with a severe bruise on his ribs, said Sergeant Lee Hee-sung of the South Korean police.
Both men in the armoured bridge carrier - Sergeant Mark Walker and Sergeant Fernando Nino - have been indicted on charges of negligent homicide for the deaths of Shim Mi-son and Shin Hyo-sun on a public road.
South Korean prosecutors questioned the two soldiers on Monday, although the US military has yet to respond to Seoul's request to try them in a local court.
If convicted in a US military court, the men face up to six years in a US prison.
A South Korean civilian court could issue a maximum jail sentence of five years on the same charge.