Her appointment was unanimously approved by the Board of Trustees on Wednesday morning. She will take office on July 1.
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Folt will become the first female president in USC's 139-year history.
Her last day at UNC was Jan. 31.
RELATED: UNC Chancellor Carol Folt's final remarks: 'I did what I thought was best, and I'm at peace with that'
She shocked the UNC System Board of Governors in January when she announced that she was stepping down and ordered the removal of the base of the Confederate monument Silent Sam in one fell swoop.
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She planned to stay on through the Spring semester, but the Board of Governors accelerated her departure.
Folt became chancellor at UNC in 2013, the 11th in the history of the nation's oldest public university.
Folt's appointment as president comes as USC contends with the fallout from a massive college bribery scheme. The school is one of several that are trying to decide what to do about students who may have been admitted through fraud.
"Of course, I also am aware that our community is deeply troubled by a number of immediate challenges," Folt said Wednesday. "I assure you that we will meet these challenges together, directly, decisively and with honesty and candor. This is a moment of responsibility and opportunity, and we will seize them both."
USC announced Monday it had placed holds on an undisclosed number of students, meaning they can't register for classes or obtain transcripts until their cases are reviewed. After a review, USC officials said they would take appropriate action, "up to revoking admission or expulsion."
"As I have come to know Dr. Folt and how she thinks, it is clear that USC has chosen a brilliant, principled leader with clarity of purpose and integrity to lead the university forward and upward," said Rick Caruso, chair of the USC Board of Trustees.
The Associated Press contributed to this report.