The valedictorian was giving his speech at the end because she forgot to introduce him earlier in the program, Gordeuk told CNN in an email.
The video shows Gordeuk standing at the podium in front of a live microphone as she says, "You people are being so rude, to not listen to this speech."
As commotion grows in the audience, she blurts out, "Look who's leaving, all the black people," prompting cries from the audience and an even larger exodus.
As the video spread through social media with the simple caption, "Yo... wow," Twitter users expressed shock, with some saying she should be fired.
The TNT Academy website describes itself as a college preparatory program for middle and high school students. The school provides credits for a high school diploma through independent study and teacher-assisted instruction, according to the website.
CNN has reached out to the Georgia Accrediting Commission, the agency that accredited the school.
The website describes Gordeuk as the school's founder, calling her an educator with more than 30 years of experience teaching in Georgia. The website says she "just completed courses" for a master's degree in "educational leadership and supervision."
Gordeuk, in a statement to CNN, apologized for her "offensive comment" and said "my emotions got the best of me."
"I deeply apologize for my actions made in the emotional state of trying to let this last student finish his speech. I take a personal interest in the success of every student that comes through our doors without regard to their race, religion or ethnicity."