Reports said the women, believed to be European, were rescued after they managed to escape from their captor and run off in different directions.
One was recaptured, but the other ran screaming from sand dunes towards a group of fishermen, witnesses said.
The man was arrested at Coorong National Park on Tuesday evening.
"She ran straight to the car yelling. She opened the back door, jumped straight in and like, 'get me out of here, get me out of here. He's going to kill us all'," fisherman Abdul-Karim Mohammed told 7 News.
He said the trio was travelling together from Adelaide to Melbourne, and had stopped at the small settlement of Salt Creek.
The second woman was found barely conscious and unable to speak, the fishermen said.
Salt Creek Roadhouse owner Adam Stewart said he encouraged the fishermen to return for the second woman after they phoned him for help.
"Unfortunately, [the women] were in pretty bad shape... We're all pretty rattled, obviously. It's a heavy event at any level. Even the police were rattled by it at a very high level," Mr Stewart told 7 News.
Details including the accused man's identity, vehicle and alleged actions during the crimes have been suppressed.
He is expected to face court again in April.
An Australian man has been charged over the alleged kidnapping and attempted murder of two female backpackers on a beach south of Adelaide.