I am afraid I cannot offer a complete answer, since I am not familiar with American academic History. But I can offer you a case-study.
Let's take a look at one of the oldest academic institutions in the United States: the College of William and Mary. It was founded in 1693, and it's located in Williamsburg, Virginia. It's can give us a good timeline from the early colonial era, Antebellum South, Civil War and even the era of Jim Crow, all in the American South.
Short Answer? Yes, absolutely, but it the opinion on it has gone back-and-forth.
It all starts in 1718 the College purchases a parcel of land and 17 slaves. It then uses the income from the tobacco grown there to provides scholarships for less wealthy students for the next 90 years. It is also very likely that students and the college also enjoyed the fruits of the labor provided by enslaved people as servants, stable hands and cooks etc. while in the city of Williamsburg.
However, in 1760, a school for black children, free and enslaved, is established in Williamsburg by The Associates of Dr. Bray (on the recommendation of Benjamin Franklin). This reflect’s WM role as an Anglican Institution, which has a duty to see to the needs of the congregation, both free and enslaved.
To top it off, Professor St. George Tucker writes a "Dissertation on [the gradual abolition of] Slavery" in 1796.
By the 1800s though, WM sells most of its slaves. The College instead begins "renting" slaves for housekeeping and other custodial duties.There are records, that in 1817, Lemon, a man owned by the College, dies. The College pays for his coffin.
However, there is a quick whiplash with in the Antebellum South era, when in 1832 Professor and future President Thomas Roderick Dew becomes becomes a renowned as the chief ideologue for the defense of Southern slavery. (In 1939, Dew's body will be reinterred in the crypt of the College Chapel, as a reinforcement of Jim Crow, and his works are praised.) Plus, in 1844, professor Nathaniel Beverley Tucker (son of St. George Tucker no less!), will defend the institution of slavery.
Through the1860-1880s, the College goes through the Civil War, most of its staff and students go off to join the Confederacy. The College also decides the invest the majority of its resources into Confederate War bonds. The subsequent Battle of Williamsburg leaves the Wren building (its main building) burned. The College is in ruins after the Civil War, President Benjamin Ewell and Malachi Gardiner, one of his black tenant farmers, keep the College officially open by ringing the College bell at the beginning of each semester. Freed people build shanties and raise livestock on the lawn in front of the Wren Building's remains.
Through the 1880s-1930s Jim Crow will exclude all black students, male and female from attending the college as well as Black employees of the College suffer wages too low to support themselves. The KKK will also gift a flag pole to College in 1926, which is placed right by the bus stop that most black employees take…
Thankfully, on February 7, 1945. A white student Marilyn Kaemmerle, editor of the Flat Hat (student newspaper), publishes Lincoln's Job Half-Done, advocating African American students at William and Mary and interracial marriage. As a reprisal, The Flat Hat is temporarily suspended and Kaemmerle loses her position. But this marks a gradual shift in the attitude of the campus. With the advent of the Civil Rigth movement, in 1951, Hulon Willis becomes the first black student to enroll at William and Mary. He graduates with a Master's in Education in 1956. Also, Edward Augustus Travis is admitted to the law school and in 1954 becomes the first African American to graduate from William & Mary. And in 1963
Oscar Houser Blayton enrolls and attends classes for his freshmen and sophomore years, becoming the College's first black undergraduate.
All of this comes from the fantastic Lemon Project, and theUniversities Studying Slavery