On Saturday, UCT announced Phakeng's appointment following a council meeting, where she received overwhelming support from members.
Her appointment comes into effect on July 1. She replaces Dr Max Price, who has held the position since 2008.
A world-renowned scholar, Phakeng joined UCT in 2016, and became deputy vice-chancellor for research and internationalisation last year.
Her academic career began at Wits, where she served as a research assistant. She became the associate professor of mathematics education, and was the founding director of the award-winning Marang Centre for Mathematics and Science Education.
She was the first black South African researcher to be appointed to co-chair a study commissioned by the International Commission on Mathematical Instruction in 2008.
Phakeng said: “I did not think I had a chance, but then I was nominated by people from different constituencies across the university, and I did not respond to it at first until a senior academic came to me and we had a discussion about why this was time to be doing this.
“We want to be a university that is inclusive and works together with the society around us and is unapologetic about being African.
"We do not want that just because people are from Gugulethu or Mitchells Plain, they feel like this university does not belong to them. As if they would have to change and be something they are not in order to get ahead. It has to be that getting ahead does not require changing one’s self, it requires just hard work.
"You can get ahead as the person you are, speaking in the accent that you do and looking the way you look.”