Brazil, who have never won the Olympic gold, started with a highly rated front three of Neymar, new Manchester City signing Gabriel Jesus, and 19-year-old Gabriel Barbosa, the Santos striker expected to head to Europe in this transfer window.
But the little-known South Africans matched them until they had Mothobi Mvala sent off just before the hour. Brazil pinned their opponents down after that but just could not score.
"That's football," Barbosa said in a TV interview after some fans in the 69,000 crowd had booed the team as they left the field. "Sometimes the ball doesn't go in the net."
Barcelona striker Neymar had two of Brazil's best chances, forcing keeper Itumeleng Khune to make diving saves to thwart two rasping drives from outside the box.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
Jesus smacked the ball off the post from two yards out when it looked easier to score, while Barbosa should have done better when he scuffed a shot with only the keeper to beat.
But a big crowd in the National Stadium in Brasilia went home unhappy after the second game of the day ended goalless.
That result was not the only surprise as their great rivals Argentina lost 2-0 to Portugal. It was the South Americans' first Olympics reverse in 13 games. Argentina were unbeaten in winning gold during their last two appearances in 2004 and 2008.
Holders Mexico drew 2-2 with Germany in Salvador, with all four goals coming in the second half.
Later in the day, South Korea put eight goals past debutants Fiji. Ryu Seungwoo got a hat trick in the demolition in Salvador, with seven of the eight goals coming in the second half.
The goals also came in the second half at the same venue earlier in the evening, when Mexico drew 2-2 with Germany.
In Thursday's final match, Nigeria beat Japan 5-4 with Oghenekaro Etebo grabbing four goals.
Earlier on Thursday, Iraq and Denmark kicked the tournament off with a 0-0 draw at a mostly empty National Stadium.
The first goals in the competition came soon after in Rio, where Honduras beat Algeria 3-2 in an enthralling match.
The opening ceremony for the Rio Games takes place on Friday but the men's soccer tournament began 24 hours earlier, a day after the women's soccer teams began their quest for gold. Twelve women's teams are in Brazil, along with 16 men's sides.
The competition is being played in Rio and six other cities.
(Editing by Ed Osmond, Ken Ferris and Frank Pingue)
