Khayelitsha police spokeswoman Anneke van der Vyver said the protest happened in the Walter Sisulu area.
"There were about 200 people who were protesting," she said.
"They burned tyres, but police moved in and extinguished the fires and dispersed the crowd.
"No incidents of violence were reported."
Van der Vyver said councillors and MECs spoke to residents, after which "everything was calmed".
Cape Town mayor Dan Plato earlier said the unenclosed toilets were removed on Monday morning after their enclosures were destroyed by ANC Youth League members and some community members last week.
Plato: Protest the ANCYL
Plato said the toilets would be replaced once residents had built enclosures themselves.
He called on Makhaza residents to burn tyres and protest against ANCYL "hooligans" and "thugs" who had destroyed the toilet enclosures.
"I want to throw it back at the community... that you need to tell those rude hooligans, those thugs, that you must march and burn tyres against those hooligans," Plato said at a media conference.
"What is happening now is that the Youth League is taking decisions on the part of the community without the community having any say in it.
"Given that the city has been prevented from building the remaining enclosures, we have resolved to temporarily remove the toilets until appropriate enclosures have been built.
"We are willing to go back and reinstall the toilets as soon as the community reaches an agreement with the Youth League."
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