Johannesburg - State Security Minister Siyabonga Cwele urged people outside the Evergreen informal settlement in Springs on the East Rand to allow delayed voting to go ahead.
This was after last-minute talks to use a church tent at the polling station until the Electoral Commission brought its own.
Surrounded by bodyguards, armed police and Ekurhuleni metro policemen carrying batons, Cwele told them the Word of God church's tent would be used until the IEC brought other tents.
About 100 people gathered there swore at Cwele, shouting things like: "The police will shit themselves today".
Cwele had held a short meeting with the pastor, Mandla Mdluli, who sought assurance that the church would be reimbursed if its tent, which the IEC wanted to use, was burnt down or damaged following arson attacks in the area from Monday.
As Cwele was led to his vehicle to visit another potential hot spot, the crowd formed a face-off with police, taunting the police to "shoot".
About 20 other people had queued to vote.
As Cwele's minibus left, police wearing bulletproof vests began chasing people through narrow passages between shacks, carrying their rifles.
The group had shouted that they wanted the release of people arrested during protests since Monday, which they said included women and children.
Stonings and protests had also taken place on Tuesday night, according to people in the group.
It was not immediately clear why the IEC could not erect its own tent or why these concerns had not been addressed sooner.
A short while later the IEC erected banners on the tent and voting began.
On Monday, a Transnet building in the neighbouring Gugulethu settlement was torched by protesters and 46 people later arrested for public violence.
There was a strong police presence with Nyala police vehicles driving around and a police helicopter circling overhead.
Cwele had come from visiting Bekkersdal earlier in the day, after it was identified by police as another potential hot spot.Download the app by visiting one of these stores.