Her dominating run came on the same day track and field's ruling body said she was undergoing a gender test because of concerns she does not meet requirements to compete as a woman.
Semenya took the lead at the halfway mark and opened a commanding lead in the last 400 meters to win by a massive 2.45 seconds in a world-leading 1 minute, 55.45 seconds. Defending champion Janeth Jepkosgei was second and Jennifer Meadows of Britain was third in 1:57.93.
After crossing the line, Semenya dusted her shoulders with her hands.
A gender test has been ordered, officials say, not because Semenya is suspected of cheating by having had a sex change operation, reports CBS News correspondent Mark Phillips, but to determine whether she has what's being called "a medical condition."
"I don't know who said it... I don't give a damn about it," Semenya told a television crew after the race.
About three weeks ago, the international federation asked South African track and field authorities to conduct the verification test. Semenya had burst onto the scene by posting a world-leading time of 1:56.72 at the African junior championships in Maruitius.
Her dramatic improvement in times, muscular build and deep voice sparked speculation about her gender. Ideally, any dispute surrounding an athlete is dealt with before a major competition. But Semenya's stunning rise from unknown teenage runner to the favorite in the 800 happened almost overnight. That meant the gender test - which takes several weeks - could not be completed in time.
Before the race, IAAF spokesman Nick Davies stressed this is a "medical issue, not an issue of cheating." He said the "extremely complex" testing has begun. The process requires a physical medical evaluation and includes reports from a gynecologist, endocrinologist, psychologist, internal medicine specialist and gender expert.
South Africa team manager Phiwe Mlangeni-Tsholetsane would not confirm or deny that Semenya was having such a test.
"We entered Caster as a woman and we want to keep it that way," Mlangeni-Tsholetsane said. "Our conscience is clear in terms of Caster. We have no reservations at all about that."
Although medals will be awarded for the 800, the race remains under a cloud until the investigation is closed, and Semenya could be stripped of the gold depending on the test results, IAAF general secretary Pierre Weiss said.
"But today there is no proof and the benefit of doubt must always be in favor of the athlete," Weiss said.
Semenya's rivals said they tried not to dwell on the issue before the race.
"I've heard a lot of speculation, but all I could do was just keep a level head and go about my business," Meadows said. "If none of it's true, I feel very sorry for her."
One thing not in doubt was Semenya's outstanding run.
"Nobody else in the world can do that sort of time at the moment," Meadows said. "She obviously took the race by storm."