Les Bleus ended a long losing run against the Springboks with a first-half attacking masterclass and a nervy second-half rearguard action, putting them in a strong position at the top of the Northern Hemisphere standings.
Antoine Dupont, shifted to fly-half amid France's injury problems at No. 10, was named Player of the Match for a commanding display that mixed vision, kicking accuracy and defensive leadership.
France struck first through wing Aaron Grandidier-Nkanang, who finished in the corner after sustained pressure through numerous phases. Full-back Theo Attissogbe then pounced on a loose ball, which had deflected off teammate Kalvin Gourgues, for the second try.
Louis Bielle-Biarrey completed the first-half scoring with a well-taken try after Dupont's pinpoint kick in behind the defence, with Maxime Lucu converting all three scores.
South Africa's only reply before the break came from a driving maul finished by hooker Jan-Hendrik Wessels, leaving France 21-7 ahead at half-time and had looking sharp with ball in hand.
The second half belonged to South Africa's forward power and looked strong even after Jasper Wiese received a 20-minute red card for a dangerous clear-out. Replacement scrum-half Cobus Reinach scored to cut the gap and Sasha Feinberg-Mngomezulu added the extras.
France were forced to dig deep, absorbing pressure and dealing with their own disciplinary issues, including a yellow card for replacement prop Regis Montagne. With around ten minutes remaining, Malcolm Marx powered over from a driving maul to make it 21-19 but replacement fly-half Manie Libbok missed the conversion that would have levelled the scores.
South Africa continued to press, but France's defence held firm and a crucial late intervention by Bielle-Biarrey forced a turnover, and Dupont helped secure possession to close out the win. France did not score a point in the second half yet showed the character required to topple the world champions.
The result was only France's second win over South Africa in their last 11 meetings and their first victory against the Springboks at the Stade de France in 21 years.
It dents South Africa's hopes of topping the Southern Hemisphere group, while strengthening France's position as Northern Hemisphere leaders ahead of their next fixture against Argentina.
Bafana Bafana head coach Pitso Mosimane found himself at the centre of attention after reacting angrily to questions about his decision to leave Mbekezeli Mbokazi out of the starting line-up against Kenya.
South Africa have surrendered top spot in the World Rugby rankings following their 21-19 defeat to France at the Stade de France in Paris.
Rassie Erasmus and Siya Kolisi refused to look for excuses after the Springboks' narrow loss to France, as they admitted they failed to play to their usual standard on a tough night in Paris.
Rome wasn't built in a day, and neither was the dynasty that Rassie Erasmus' Springboks are playing in.
