The 18-year-old Semenya took the lead halfway through the race and won in a world leading 1 minute, 55.45 seconds, beating defending champion Janeth Jepkosgei by a massive 2.45 seconds. Jennifer Meadows of Britain took bronze.
Olympic champion Pamela Jelimo was eliminated in qualifying.
The IAAF requested the gender test on Semenya about three weeks ago amid speculation she does not meet the requirements to compete as a woman.
The request came after Semenya burst onto the scene by slicing her personal bests in the 800 and 1,500 by huge margins.
IAAF spokesman Nick Davies stressed that "it's a medical issue, not an issue of cheating."
He said the "extremely complex, difficult" test has been started but that the results were not expected for weeks.
The verification test requires a physical medical evaluation, and includes reports from a gynecologist, endocrinologist, psychologist, an internal medicine specialist and an expert on gender.
"So we're talking about reports that are very long, very time consuming," Davies said.
South Africa team manager Phiwe Mlangeni-Tsholetsane would not confirm or deny that Semenya was having a gender test, but said "there was no cheating on our part."
"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."
Semenya qualified for Wednesday's final with a top time of 1 minute, 58.64 seconds, and posted the world's best time this year of 1:56.72 three weeks ago at the African junior championships in Bambous, Mauritius.
It was not immediately clear what will happen now Semenya has won the gold medal if the test results later determine she does not meet the requirements to compete.
"I can't say that if 'X' happens in the future that we will, for example, retroactively strip results. It's legally very complex," Davies said.
"If there's a problem and it turns out that there's been a fraud ... that someone has changed sex, then obviously it would be much easier to strip results," Davies added. "However, if it's a natural thing and the athlete has always thought she's a woman or been a woman, it's not exactly cheating."
He said a decision in such instances is "done on a case by case basis."
"It's something that would have to be considered by the legal experts at that time," Davies said.
