A number of weapons have been recovered by SAPS According to national police spokesperson Brigadier Vish Naidoo, a group of attackers indicated to those inside "that they were coming to take over the premises".
Police say more than 30 guns were found and the attack by a group of armed people "may have been motivated by a feud" between church members.
Thirty arrests were made and more than 25 firearms seized, police said, adding hostage negotiators were still at the scene.
He said during the response, joint law-enforcement agencies managed to rescue men, women and children who are said to be living in the compound and were held hostage.
The national police commissioner says the response by security forces "averted what could have been a more severe bloodbath".
Police have arrested several suspects while still engaging hostage negotiators.
It is unclear why the hostages were being kept, though there are rumours that the incident relates to a dispute between church members.
"Trouble has been brewing at the church following the death of its leader‚ Glayton Modise‚ in February 2016", The Sowetan newspaper reported in 2018.
The International Pentecost Holiness Church, which bases its headquarters in Zuurbekom, is among the largest African initiated Christian churches in Southern Africa with three million members.
It has not yet known been confirmed if today's hostage situation relates to the ongoing row.
The church was founded in 1911 by Abner Blackmon Crumpler and Benjamin H Irwin following the merger of two older denominations.