The two men were heading for an Islamic convention in Atlanta, Georgia, the Johannesburg-based Sunday Times reported.
The paper added that after a 17-hour flight from Johannesburg to attend the convention hosted by the Atlanta Islamic Institute, businessman Musa Sulayman and cleric Mulana Ahmad Sulayman Khatani were detained by immigration officials, fingerprinted and photographed.
"Their passports, credit cards, invitations to the conference and other documentation were photocopied," the newspaper said.
Sulayman, who is 66 and has a full white beard, told the Sunday Times he was sent back home after enduring "five hours of hell, uncertainty and embarrassment".
Khatani, 33, was detained and spent more than 34 hours in a cell with four criminals before being deported, the newspaper said.
"My documentation was all in order. It was quite clear that I was discriminated against because of my beard and appearance"
Ahmad Sulayman Khatani,
South African cleric
Sulayman said guards escorted them when they needed to go to the toilet.
Sulayman, who lives in Durban, said he was questioned about trips he had made to Saudi Arabia, Malaysia and Indonesia.
"My documentation was all in order," he said. "It was quite clear that I was discriminated against because of my beard and appearance."
The two were among the first foreign visitors subjected to a new security check known as US-VISIT, US Visitor and Immigrant Status Indicator Technology.
The acting US consul in Durban, Liam Humphrey, told the Sunday Times visas issued abroad could be "overridden by the immigration service, which is incorporated into (the department of) homeland security".