The Independent Police Investigative Directorate (Ipid) is now investigating the matter.
Details surrounding the incident have not been divulged by authorities.
Police shot the man in the chest on Monday.
Four people were arrested on charges of public violence after residents of Imizamo Yethu informal settlement ran amok, stoning and overturning cars, burning another car and damaging City property.
They demanded that rebuilding in the area be sped up following a devastating fire in March which left 15 000 mense destitute.
Residents stopped their protest after Cape Town Mayor Patricia de Lille addressed them late on Monday and held a meeting with community leaders.
“Together with the community leadership we agreed that we are going to accelerate re-blocking across three areas [Madiba Square, the Shooting Range site and Donste Yakhe]. We will work in all three areas at the same time,” De Lille said.
“We are assigning a new programme management team to facilitate and oversee all line departments in the area.”
She condemned the acts of violence during the protest.
“There is no justification for the violence which took place over the past three days. Some of the damage incurred on Monday includes the destruction of the site office and equipment of the civil contractor in addition to the petrol bombing of a sewerage pipe.
“The people of Imizamo Yethu cannot afford these kinds of setbacks.”