An unidentified black woman was about halfway up the more than 30-foot steel flagpole just after dawn Saturday when State Capitol police told her to come down. Instead, she continued up and removed the flag before returning to the ground.
The woman and another man who had entered the wrought-iron fence surrounding the flag were arrested.
The flag, which is protected by state law, was raised again a short time later. A rally by flag supporters was scheduled for later Saturday.
Calls for removing the flag have been renewed since nine black churchgoers were killed in what police characterized as a racist attack at a Charleston, South Carolina church last week.