The confirmation was made by the prime minister, Jorge Jesus, who said the test which was sent to Gabon came back positive.
No other information was given about the patients.
This makes Sao Tome the 52nd country in Africa to confirm a case, leaving Comoros and Lesotho virus free.
The continent as of Monday night had a total of 9,864 confirmed cases, 486 deaths, and nearly 1000 recoveries.
In Libya, a rebel leader, Mahmud Jibirl, who led the forceful removal of Libyan dictator Muammar Gaddafi in 2011, died on Sunday after contracting the deadly virus.
The 68-year old had been hospitalised for two weeks in Cairo, Egypt – the secretary of the Alliance of National forces party, Khaled al-Mrimi, confirmed.
Hisham Wagdyn, the director of the Egyptian hospital, revealed that Mr Jibril was “admitted to the hospital on March 21 after suffering a heart attack before testing positive for the coronavirus and being quarantined.”
Mr Jibril died in Egypt which has a total of 1,322 confirmed cases, 85 deaths, and 259 recoveries. His country Libya has a total of 18 confirmed cases, 1 death, and 1 recovery.
Meanwhile, the World Health Organisation’s Director-General Tedros Adhanom, in a press briefing called for unity across all nations in the world.
“We have said consistently that we’re all in this together, and we can only succeed together. We need an all-of-society approach, with everyone playing their part,” he said.
In regard to a statement made earlier by French scientists who suggested the use of Africans as “guinea pigs” for COVID-19 research, he refuted this saying “Africa cannot and will not be the testing ground for any vaccine. The hangover from such colonial (mentality) has to stop.”