Foreign Affairs spokesman Ronnie Mamoepa said South Africa's ambassador to Gabon, Mokgethi Monaisa, and Foreign Affairs deputy director-general Kingsley Mamabolo were in Equatorial Guinea.
"The two officials visited Du Toit in prison and confirmed that he is alive.
"This puts paid claims that a South African has died in detention in Equatorial Guinea," he said.
Mamoepa said the two officials were still in the country on Thursday afternoon. He could not comment further about the visit.
The French news agency AFP earlier quoted the Spanish newspaper El Pais as reporting that Du Toit had died on Wednesday after being tortured.
He is the alleged leader of a group of coup plotters arrested in Equatorial Guinea last week.
A man identified as Du Toit appeared on television in the central African country last week. He reportedly said he had led a group of mercenaries there on a mission to abduct President Teodoro Obiang Nguema and force him into exile.
Equatorial Guinea government spokesman Antonio Fernando Nve Ngu said on Thursday an alleged German mercenary, one of the 15 supposed plotters, had died of cerebral malaria.
AFP reported that Gerhard Eugen Nershz was transferred Tuesday from Malabo's central jail to hospital on the recommendation of the prison doctor.
"He received the appropriate care, but died a few hours later of cerebral malaria with complications," Nve Mgu said in a statement read on state radio.
Apart from Du Toit, the Equatorial Guinean authorities have identified the suspects only by giving a list of nationalities, saying they came from South Africa, Angola, Armenia, Sao Tome and Principe and Germany - Sapa.
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