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A week after a 38-18 defeat against New Zealand, France failed to dominate a South Africa side who were comprehensively beaten by Ireland last Saturday and conceded their sixth consecutive loss to the Springboks.
South Africa scored two tries through Dillyn Leyds and Jesse Kriel with Handre Pollard, who missed four kicks, adding eight points with his boot.
Flyhalf Anthony Belleau scored a try, a penalty and two conversions while Baptiste Serin added a late try for the home side.
France's most successful club coach with four European Cups and nine national titles with Toulouse, Noves has lost 13 of his 20 games in charge of Les Bleus since he was named after the 2015 World Cup.
France next take on Japan at the brand new U-Arena in Nanterre, on the outskirts of Paris, next Saturday.
A few days after France won the right to host the 2023 World Cup at the expense of South Africa and Ireland, Les Bleus looked hardly like a team able to lift the trophy in 2019.
France got off to a dominant start but fluffed a good try chance early on, while South Africa touched down at the end of their first foray into the French half when Leyds dived over for his first try with the Springboks.
Pollard added a penalty midway through the first half.
Les Bleus responded with Belleau, who sold the defence a dummy before touching down between the posts and adding the extras.
South Africa were then penalised for offside but Belleau missed the 42-metre penalty as the visitors stayed ahead.
Pollard missed two consecutive penalties as France stayed in the hunt.
Early in the second half, France dominated and they were rewarded when Belleau's penalty gave them the lead for the first time.
Pollard missed yet another routine penalty but slotted home another to put South Africa ahead again with just over 20 minutes left.
Kriel scored South Africa's second try at the end of a long dominant spell that the French defence failed to contain.
The Stade de France went almost silent and France never seemed able to turn the situation around.
They were vocal again when substitute scrumhalf Serin touched down after fine work by the French forwards.
Belleau converted to reduce the deficit to one point three minutes before the end.
South Africa then did a good job keeping the ball in the closing stages to snatch a deserved victory.