Suber announced her retirement from her position at the historically black school, but said she would stay on for another two months.
Board of Trustees chairman Trustee Chairman Rodney Gaddy told reporters at a news conference Monday that the board felt a change was needed right away.
Gaddy said an interim president will be named soon.
St. Aug's has had a number of problems recently. The Southern Association of Colleges and Schools is reviewing the school because of its financial condition. Full-time equivalent enrollment fell from 1,387 in fall 2012 to 1,267 last fall, when an audit showed a $3 million drop in tuition revenue.
Last Thursday, Suber fired the school's vice president of business and finance. Last month, she placed the provost on leave. Two other vice presidents left last year.
Suber had been president for 14 years.