Under white minority rule the Regina Mundi church was a focal point for anti-apartheid activists.
During the 1976 Soweto uprising police entered and fired on those who had taken refuge.
No-one was killed but many were injured and the building was damaged.
On Sunday’s day of prayer for Nelson Mandela, there was standing room only as hundreds packed into the church.
“He’s done a lot for us. We are like this because of him. We were suffering, we were not getting what we want, but now we are free and get anything that we want any time,” said a female worshipper.
Father Sebastian Rossouw told the congregation that Mandela was a guiding light for nation.
“Madiba for us here in South Africa and I think in the world has been that prophet, has been that light for us to say that our God is still with us, our God still listens to our prayers, his promises still come true to us,” he told euronews.
The tributes and prayers for Mandela have been echoed elsewhere – including in affluent white areas where such recognition would have been unthinkable two decades ago.
As a choir sang praise for Mandela behind him in the church, euronews correspondent François Chignac
said: “All day long in Johannesburg and in all the city’s churches, like here in the heart of Soweto, hundreds of people have come to pay their last respects to Nelson Mandela.”