The US army lieutenant colonel was attacked by three men carrying a knife who swore at him and told him that US forces should leave South Korea.
The attack, which occurred on Sunday night, came a day after 50,000 South Koreans rallied in the capital Seoul.
Analysts said the protests could influence South Korea's presidential election on Thursday, with both the front-runners calling on the US to revise the agreement which governs American troops in South Korea.
The knife attack took place outside the US army base at Yongsan, which has been targeted by protesters several times since a US armoured vehicle ran over and killed Shim Mi-son and Shin Hyo-sun on a public road.
The US soldier told police that three South Koreans in their 20s began swearing at him, pushed him against a wall, punched him and "brushed" his side with a knife.
The soldier, who was named as Steven A. Boylan, received treatment for minor injuries in a US military hospital.
Earlier on Sunday, three US soldiers were involved in an argument with South Koreans after a traffic dispute. Each group accused the other of starting the fight. There were no arrests.
The incidents will add to tensions over the US presence in South Korea, where 37,000 troops are stationed to guard against the threat posed by Stalinist North Korea.
At present those troops are subject to an agreement known as the Status of Forces Agreement, which usually means that any charges against US troops are heard in US military courts.
Marchers at the Saturday protests in Seoul called for the agreement to be revised to give South Korean courts jurisdiction.
They also wanted the two men involved in the accident - which a US court martial found not guilty of negligent homicide for the girls' deaths - to be tried in a South Korean court.
He was able to twist away, but sustained a minor cut to his
left side where the knife grazed him
US army statement
The BBC's Caroline Gluck, in Seoul, says it was the largest demonstration since the two soldiers, whose armoured vehicle hit the girls, were acquitted in November.
Another of the protesters' demands appeared to have been met last week when US President George Bush expressed his regret over the deaths in a telephone conversation with South Korean President Kim Dae-Jung on Friday.
But his words failed to appease the crowd which marched through Seoul on Saturday.
Carrying candles in mourning, demonstrators cheered and applauded when speakers demanded more South Korean jurisdiction over US troops.
There were also angry words for President Kim Dae-jung, who was called a "US puppet".
Large US flags were held aloft by the crowd and torn apart.
Our correspondent says the government has opened talks with US officials to improve the code, but their efforts so far have not calmed the public mood.
Public anger has also fed into campaigning for the presidential poll.
Roh Moo-hyun, 56, the candidate for the ruling Millennium Democratic party, has said the US alliance must be brought up to date.
His main opponent, Lee Hoi-chang, who is seen to share the US' hard-line stance towards North Korea, has also made sure to publicly condemn the court's verdict.