Goals from Bongani Khumalo and Katlego Mphela gave South Africa a commanding lead while France also had midfielder Yoann Gourcuff sent off.
A second-half goal from substitute Florent Malouda was scant consolation for France, who finished bottom of Group A.
Some would question whether France should have been in the competition in the first place following Thierry Henry's handball against the Republic of Ireland that clinched their place in South Africa 2010.
But despite their ill-gotten spot in the tournament, their stay has been nothing sort of a disaster.
France went into this match with a host of embarrassing problems to contend with that had unsettled their preparations.
Coach Raymond Domenech had a very public fallout with striker Nicolas Anelka at half-time during their 2-0 defeat to Mexico with the latter being expelled from the squad.
Then there was the training ground row between Patrice Evra and fitness coach Robert Duverne on Sunday.
The French camp has certainly been an unhappy one, with players even refusing to train with Domenech.
Evra's outburst and subsequent remarks earned him a dressing down from Domenech in the form of a demotion to the substitutes' bench.
The Manchester United defender was one of six changes while Henry had to be content with a seat alongside him.
While France arrived in Bloemfontein looking dishevelled and thoroughly unhappy to be there, their opponents arrived in buoyant mood.
The hosts were determined to finish this tournament in style and certainly started the brighter of the two teams.
And they took a deserved lead in the 20th minute when Khumalo headed home from Siphiwe Tshabalala's corner.
The giant Supersport United defender could not believe his luck as France goalkeeper Hugo Lloris flapped at the cross and took full advantage.
The match took another turn for the worse for France when they were reduced to 10 men in the 25th minute when Gourcuff was sent off for raising his arm in a challenge with MacBeth Sibaya.
Mphela then made it 2-0 when he bundled the ball over the line to finish a move involving Tshabalala and Tsepo Masilela.
Malouda tapped in from close range after Franck Ribery supplied the cross to bring the curtain down on Domenech's reign in charge of France.
But Uruguay's victory over Mexico meant that both France and South Africa will not be taking part in the knockout stages.
France (4-4-2): Lloris; Sagna, Squillaci, Gallas, Clichy; Gourcuff, Diarra (Govou 82), Diaby, Ribery, Cisse (Henry 55), Gignac (Malouda 46).
Subs (not used): Mandanda, Abidal, Reveillere, Planus, Evra, Valbuena.
South Africa (4-4-2): Josephs; Ngcongca (Gaxa 55), Mokoena, Khumalo, Masilela; Pienaar, Sibaya, Khuboni (Modise 78), Tshabalala; Mphela, Parker (Nomvethe 68).
Subs (not used): Walters, Booth, Thwala, Sangweni, Davids, Letsholonyane, Moriri.