The plaque is adjacent to the statue of Rhodes in Oriel College, where thousands of Rhodes Must Fall campaigners have protested to have the statue removed due to the politician and businessman’s views on colonialism and race.
Historic England previously said that the plaque did not merit legal protection as it lacked the “richness of detail” to make it of national interest.
But the culture secretary felt the plaque was of “special historic interest”.
“We are committed to retaining and explaining our heritage so people can examine all part of Britain’s history and understand our shared past,” a Department for Culture Media and Sport (DCMS) spokesperson said.
Rhodes, a 19th century merchant and politician in southern Africa, was a student at Oriel and left the college £100,000 (£12.5m today) when he died in 1902.
A staunch supporter of British imperialism, Rhodes founded Rhodesia (now Zimbabwe and Zambia) and the De Beers diamond mining company. His policies as prime minister of the Cape Colony are seen as having set the way for apartheid.
Academic and experts in colonial history have accused the government of “whitewashing” the severity of colonialism and deliberately stoking culture wars as a result of the decision.
Kim Wagner, professor of imperial history at Queen Mary University of London, told The Guardian: “This is simply what one would expect from Nadine Dorries and a discredited government, which has nothing left but the pursuit of its inept culture-war project.
“Cecil Rhodes has become a rallying point for imperiophiliacs, and the slogan to ‘retain and explain’ is just part of the ongoing effort to whitewash his legacy and that of the empire more generally. Luckily, most of us don’t get our history from statues or plaques.”
Last year, the college said it would not remove the statue of Rhodes, despite an independent commission’s recommendation that it be taken down.
Oriel College responded that it would not remove the statue due to costs and “complex” planning processes.