Pastor Steven Anderson made headlines in the US after he praised the shooting that left dozens dead at an Orlando gay club in June.
South Africa's home affairs minister said after consultation with leaders of the nation's lesbian, gay, bisexual and transgender communities, he decided Anderson is not welcome there.
Anderson had intended to visit South Africa this week, until he learned of the news.
Americans traveling to South Africa don't need visas as part of a waiver program. Despite the program, the pastor and his associates will not be allowed into the nation.
'They promote hate speech'
The South African official used harsh words to explain the decision to ban the church leader.
"I have identified Steven Anderson and members and/or associates of his church as undesirable persons," Home Affairs Minister Malusi Gigaba said in a statement.
"I have withdrawn their visa exemption status, enjoyed by all Americans ... on the basis that I am certain they promote hate speech as well as advocate social violence."
Homosexuality is illegal in most African countries
based on remnants of sodomy laws introduced during the British colonial era and perpetuated by cultural beliefs.
But South Africa is one of the more progressive nations in the continent on the issue, and was the first African country to impose a constitutional ban on discrimination based on sexual orientation.
Pastor headed to Botswana
South African anti-discrimination legislation is there to "prevent and prohibit hate speech and harassment," which is why Anderson will not enter the country, Gigaba said.
Anderson leads the Faithful Word Baptist Church in Tempe, Arizona.
In a message on Facebook
and YouTube, Anderson said he's aware of the ban and is "sorry for people who live in South Africa."
He said he's moving on to his next destination: Botswana.
"Stand by for reports of multitudes saved in Botswana, where religious freedom still exists," he posted.