Kenya's Margaret Wambui, bronze medallist at both the world indoors and Olympics a year ago, won that heat, but Arzamasova's season's best of 2:01.92 was not fast enough to see her bag one of the faster loser places.
Poland's Angelika Cichocka produced a remarkable finish, cutting in from the outside of lane two to the inside of lane one to sneak second place in heat two and an automatic slot.
Usain Bolt blames 100 meter loss on starting blocks
Jamaican team doctor Dr Kevin Jones later confirmed that Bolt had suffered from "cramp in his left hamstring". "It was ridiculous. There will be a fair amount of emotion from the stands as Mo Farah also runs in his last track race - the 5,000 metres final.
Hitting the home straight, Wilson and Niyonsaba were neck and neck before Semenya moved smoothly outside the lead duo and motored through the line for a convincing victory.
Semenya is back in the spotlight following a study funded by the IAAF and the World Anti-Doping Agency (Wada) that showed female athletes with naturally high levels of testosterone enjoy a competitive advantage of up to 4.5 percent over their rivals.
Semenya, a bronze medallist in the 1500m in London as she attempted an audacious double, clocked an impressive 1min 58.90sec, looking incredibly comfortable as she broke with 20 metres to run. It was the American and the Burundian who sat at the front who stayed at the front, though with the final lap approaching those two and Semenya and Wambui took off from the rest of the field, and it was clear the battle for the medals was between those four.