Wallace had in mind the exclusion of blacks from white-only institutions. Today’s racial segregation, by contrast, consists of ethnic groups walling themselves off within institutions. In the past two years the National Association of Scholars surveyed 173 colleges and universities, public and private, in all 50 states. We found 46% of schools segregate student orientation programs, 43% segregate residential arrangements, and 72% segregate graduation ceremonies. Though these arrangements are ostensibly voluntary, students can’t easily opt out. The social pressure to conform is overwhelming.

This kind of racial separatism on campus isn’t new. We pursued case studies of Yale, Wesleyan and Brown universities, where we found that black students began to organize exclusive groups with separatist agendas as early as the 1960s.

Begin with Yale, the subject of a 210-page study released by NAS this week. The Black Students Association at Yale, or BSAY, was founded in 1964 as the Yale Discussion Group. Black students started the organization because they felt Yale recruited them merely for show. The accusation may have been unfair but it touched something real.

In 1964 Yale’s newly appointed president, Kingman Brewster, declared an all-out “effort to cure racial injustice.” This meant discarding Yale’s old policy of admitting only highly qualified black students in favor of aggressive outreach to the inner cities. Brewster’s like-minded admissions dean, R. Inslee “Inky” Clark, openly set forth a plan to enroll black students regardless of their test scores or other evidence of academic achievement. Brewster and Clark believed they could turn anyone into a Yale man. (The university didn’t admit female undergraduates until 1969.)

The new zeal to boost numbers brushed aside hard questions about college readiness and cultural adjustment. The results were catastrophic for the students. More than a third of the 35 black students Yale enrolled in 1966 dropped out during their first year, and many others lagged behind academically and felt unwelcome.

To stem the exodus, Yale set up a summer remediation program for black students. It did little to encourage their academic success, but it unexpectedly reshaped relations between black students and the university. The program isolated the black students as a group and gave them a sense of solidarity and shared grievance.

Out of this seedbed sprang BSAY, which was Yale’s first racial identity group. BSAY found its voice by demanding that Yale provide an ever-greater number of accommodations, including separate advisers, a separate orientation, and a separate center in a separate building. BSAY also became the leading advocate for a separate curriculum—the African-American studies program—that entailed hiring new faculty members with appropriate qualifications. A new world began to open up at Yale bearing a strange resemblance to the “separate but equal” arrangements that the Supreme Court had ruled unconstitutional in 1954 in Brown v. Board of Education.

Though this happened more than 50 years ago, the pattern set down in the turmoil of the late 1960s continues. BSAY’s goal wasn’t a university where racial difference ceased to matter, but a university that aggrandized race and celebrated separation. Brewster agreed to almost anything activists wanted, apparently hoping a golden age of racial integration would follow.

Instead, BSAY grasped that racial intimidation yields rich rewards. The intimidation expanded beyond BSAY itself to a broader coalition of identity groups. Yale now steers its course with a compass of group rights, with each group asserting its own demand to be compensated for past wrongs. The most famous example is the 2015 mobbing of Prof. Nicholas Christakis over Halloween costumes. Yale President Peter Salovey responded by praising the “affirming and effective forms of protest,” and the trustees soon set aside $50 million to meet protesters’ demands.

Yale is a private institution with abundant resources to deploy as it pleases. But Yale is also one of the templates for American higher education as a whole. Its readiness to appease racial separatists who hold the ideal of racial integration in contempt has become the campus norm.

Wesleyan University in Middletown, Conn., became one of the first schools to embrace residential segregation when it created the Afro-American House (now called the Malcolm X House) circa 1968. In 1972 Cornell began accepting black students to its Ujamaa Residential College, a 144-resident building for blacks who have “personal knowledge” of the black experience. Other elite schools, such as Columbia University (Pan African House), Massachusetts Institute of Technology (Chocolate City), the University of California Berkeley (African American Theme Program), Stanford University (Ujamaa), and Amherst College (Charles Drew House), made similar arrangements. In 2016 the University of Connecticut opened the Scholars House for black male students. The crush of protests across academia in fall 2015 was driven by racial organizations composed of students primed to see themselves not as individuals but as members of persecuted racial groups.

Today’s campus segregation puts people in a racial box. And like other forms of segregation, it has been a major source of tumult in higher education across the decades. Institutions of higher education should stop deliberately balkanizing their student bodies, and work instead to unify them around the common purpose of seeking truth and knowledge.

Mr. Wood is president of the National Association of Scholars. Mr. Pierre is a research associate at the association and primary author of its new report, “Separate But Equal, Again: Neo-Segregation in Higher Education.”