Police and Interior Ministry units rushed to the court on Wednesday, where the crowd had broken windows in its efforts to get into the building. A few bottles with flammable liquid could be seen littering the area.
Witnesses said the crowd had stormed the building to eject the protesters - who had occupied it since 22 April - and allow the court to resume its work.
It was the most intense unrest to break out in Kyrgyzstan since the March uprising that ousted longtime President Askar Akayev, who was replaced by acting President Kurmanbek Bakiyev.
A woman who identified herself only by her first name, Nurjamal, said she had come from a nearby village, Kara-Balta, to the court.
She said that prisoners who had earlier been granted amnesty were waiting in vain to be freed but that the court had not been able to deal with their cases.
"We are not for any lawmakers but for the court. What will happen if people keep occupying government buildings?" Nurjamal said.
Once inside the building, the crowd started throwing out blankets and other items the occupiers had used.
Supporters of the defeated parliamentary candidates had vowed that they would not leave until the Supreme Court judges resigned.