"Much has been said about the so-called "blackface" incident at our Heemstede Women's Residence two weeks ago. I would like to use this opportunity to contribute to the discussion," Stellenbosch University (SU) Rector and Vice-Chancellor Prof Wim de Villiers writes in a message to the University community.

"First, I wish to reiterate the regret that Stellenbosch University (SU) feels over what the two students in the eye of the storm had to endure. That was a most unpleasant experience, and I am very sorry about their ordeal.

"An internal investigation by our Unit for Equality in the week following the incident completely exonerated them (see statement). They had used purple body paint to resemble extra-terrestrials for a space-themed party at the residence – with no intention to offend. However, a photograph posted on social media was interpreted as "blackfacing", which in light of the country's history of racism caused major dismay. Some of their fellow students lodged complaints, and the University's relevant structures got involved immediately.

"Meanwhile, allegations have been raised that the University dealt with the situation incorrectly. We have taken note of that and this week decided to launch an investigation by an independent commissioner (see statement). We want a comprehensive look at every facet of the incident, including the University's handling of the matter. Specific recommendations to the University will flow from the investigation.

"The two students have returned to the residence after their temporary suspension was lifted, and can now focus on their studies once more, which I am very pleased about. The University will continue to support them as it has done throughout.

"Last week, a Sunday paper asked: What if one of the two students was my daughter? I thought hard about this, and to a certain extent they are indeed my daughters. As the head of the University, I have many daughters and sons. I realise this could sound terribly patriarchal, but let me explain.

"At my inauguration last year, I said that the best interest of the student is the only interest of a university. Those words were adapted from a slogan used by the Mayo Clinic in the United States, namely that the best interest of the patient is the only interest.

"We have a major responsibility to young people who come to study at Stellenbosch University – to walk the path of knowledge with them in preparation for their professional lives one day, and for their lifelong contribution to society. This responsibility extends to all our students. I have many daughters and sons, and every single one matters. The students who were offended by what was initially considered to be "blackfacing" are also my daughters and sons. We need to acknowledge everyone's pain; none is more legitimate than the other. We must strike this balance.

"I want every student's time at the University to be enriching and fulfilling. I do not want them to have any unpleasant experiences. Of course, life is not all moonlight and roses, but as an institution – including the individual staff members and students who are part of it – we should constantly try to do what is right and avoid what is wrong. Sometimes, things do go wrong. Nothing and no one is perfect, but we need to put right what is wrong, and take lessons from the experience. A university is a place of learning, and we have learnt plenty on various levels the past while. Procedures need to be followed, codes of conduct must be respected – and that applies to everyone in equal measure.

"People feel very strongly about certain matters – and that is fine. From the beginning, I have encouraged open discussion at SU. A culture of promoting bold debate and critical discourse about societal challenges lies at the heart of university life. But how we engage with each other should reflect such values as empathy, shared accountability and leadership in service of others, as set out in the University's Institutional Intent and Strategy. This will create safe spaces for interaction without intimidation, manipulation, threats, racism, sexism, homophobia and other forms of discrimination and dehumanisation.

"I have been shocked by the vicious abuse of members of the University community in the wake of the incident, and this should stop.

"Open discussion involves talking and listening. I hear black students saying they are being excluded by an institutional culture that is unwelcoming toward them. I hear white students saying they feel abandoned by the University and suffer a loss of identity as a result. However, I also hear black and white students taking a firm stance against exclusion and discrimination – which is heartening. All over campus, I see young people get along – despite apparent differences. I see young people treating each other with respect and dignity – regardless of colour, religion, gender or sexual orientation.

"I am certainly not blind to the challenges we are facing. I see prejudices continuing. I see the divides of the past resurfacing, and new ones forming – among other things from the way people discuss SU on social media in particular, and I take note of the nature of these discussions.

"However, I also see a new generation that accepts the inevitability of change and the necessity to continually adapt to new circumstances. I see thought leadership in action, and that fills me with optimism about the future."

• A longer version of this message has been published by Die Burger as an op-ed.