About 15,000 people had gathered for a rally on Saturday night demanding that the government withdraw its decision to lift a ban of American beef.
But the protest turned violent when some people used ropes to try and move police buses that were used as barricades to prevent them from marching on the president's Blue House office.
Many of the injured suffered head wounds from the stones that were being thrown and were taken to hospitals in ambulances, according to witnesses on the scene.
A police spokesman said more than 30 troops were injured in the prolonged overnight clashes, while protest organisers claimed that more than 100 citizens were hurt.
Police said that they arrested about 50 protesters on charges of assaulting police and illegally occupying streets.
Health fears
Activists have held daily protests sparked by the fears of possible health risks, such as mad cow disease, from US beef.
Imports were banned in late 2003, when the first case of mad cow disease in the US was discovered.
Condoleezza Rice, the US secreatary of state, was inundated with questions about the issue during an official visit to Seoul on Saturday
"I want to assure everyone that American beef is safe," she said during a news conference with Yu Myung-hwan, her South Korean counterpart.
"We will continue to work with you to have consumer confidence in that matter."
In the wake of public outrage over plans to resume shipments of American beef, the South Korean cabinet offered to resign and the president reshuffled his senior advisers.