Her parents were also active in civil rights and often participated in local meetings, donations, and activities in the community that promoted equality and desegregation. As a teenager, Malone was often involved in community organizations to end racial discrimination and worked closely with local leaders of the movements to work for desegregation in schools. In February 1961, she enrolled in Alabama Agricultural and Mechanical University, one of the few colleges for black students in Alabama.

She attended Alabama A&M for two years and received a Bachelor's degree in Business Education. She had wanted to pursue a degree in accounting, a field of study not offered by Alabama A&M at the time. To earn an accredited degree in accounting, Malone would have to transfer to another university. After applying to the Mobile branch of the University of Alabama, Malone and her family had been visited by two white men who had claimed that they were representatives of the state. They disclosed that her attempts to apply to the Mobile campus and integrate with the school had instigated violent retaliation from the local white community from which the family would not receive much protection. The threat to her safety did not deter Vivian Malone from continuing to support integration in the university and she persisted in applying to the University of Alabama to earn a degree in accounting. The NAACP Legal Defense and Educational Fund of Alabama organized an opportunity with Malone to enroll her in the University of Alabama's School of Commerce and Business Administration to earn her accounting degree. After two years of deliberation and court proceedings, Malone and Hood were granted permission to enroll in the university by order of District Court Judge Harlan Grooms in 1963.

On June 11, 1963, Vivian Malone and Hood, accompanied by United States Deputy Attorney General Nicholas Katzenbach and a three-car motorcade full of federal marshals, arrived at the University of Alabama's campus with the intention to enroll. Vivian Malone was only 20 years old when she enrolled in the university with Hood. Governor Wallace was waiting for them on campus and blocking the entryway to Foster Auditorium, flanked by a group of state troopers. As Malone and Hood waited in a car, Deputy Attorney General Katzenbach and a small team of federal marshals confronted Wallace to demand that Malone and Hood be allowed entry by order of the federal court and for Wallace to step aside. Wallace had not only refused the order, but he interrupted Katzenbach; in front of the crowds of media crews surrounding him, Wallace delivered a short, symbolic speech concerning state sovereignty, claiming:

“The unwelcomed, unwanted, unwarranted and force-induced intrusion upon the campus of the University of Alabama...”

After seeing that Wallace would not step aside, Katzenbach called upon the assistance of President John F. Kennedy to force Wallace to permit the black students' entry into the university. President John F. Kennedy federalized the Alabama National Guard later the same day, which put them under the command of the President, rather than the Governor of Alabama. Malone and Hood then entered the building, albeit through another door. Two years later, in 1965, she received a Bachelor of Arts in business management and became the first black student to graduate from the University of Alabama.