Kent University Students Union was facing a backlash after students pointed out that that neither Malik nor Khan was black.
The UK organisers of Black History Month said they were “deeply disappointed” by the university’s choices.
The student union at Kent University said it aimed to ‘empower’ students through its Black History Month, where it chose six public figures to represent diversity, at a number of events throughout October.
Black History Month tweeted: “Deeply disappointed at Kent University’s ill thought and misdirected Black History Month celebrations.
“With Asian Heritage Month being observed by a growing number of countries in May, will black icons be celebrated then?”
Khan was born in Tooting, south London after his parents migrated from Pakistan to Britain.
Malik, the former One Direction heartthrob, was born in Bradford, in 1993 to Pakistani-English parents.
Despite the university’s apology, students described the mistake as a “national embarrassment”.
Benjamin Smith wrote: “At this point Kent Union has become a national embarrassment.
“From what I’m seeing, this post doesn’t really cover the extent of the offence you’ve caused and comes across as a bit patronising.”
Other names on the list include Dame Kelly Holmes, Sir Trevor McDonald, Shirley Bassey and Arthur Wharton, Britain’s first black professional footballer.
Kent Union president Rory Murray apologised to students who were “upset, uncomfortable or offended”.
He said: “I want to apologise on behalf of Kent Union to any individuals who were upset, uncomfortable or offended by the image shared.
“There was no intent for this to happen and I am very sorry to anybody who felt this way.”
The university, which counts Shadow Foreign Secretary Emily Thornberry and actor Orlando Bloom as alumni, has 11 per cent of black students and ten per cent black staff.
A statement from the union said: “As you are aware, last night we removed the post about Zayn Malik. We would like to unreservedly apologise for any offence or upset that was caused by this post.
“In the planning stages of Black History Month, we worked with students to develop a campaign that celebrated a range of ethnic cultures.
“However we can see that many of our students disagree with the direction the campaign took. We made a mistake.”