They were beaten 12-0 by Argentina in their first match of the day, with the last two tests by Los Pumas Sevens, who went on to take Pool B and drop the Blitzboks to third place and out of Cup competition.
That meant a ninth quarter-final against Kenya, but despite another Siviwe Soyizwapi and half-time lead, Kenya scored three times in the second half to win.
The Blitzboks will play Canada on the 13thTh The semi-finals take place at 19h22 on Friday (SA time).
In the Pool B decider against Argentina, the lack of scoring opportunities was too much for the South Africans.
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They defended well and at the break the score was tied 0-0. The second half was a tight affair, but Argentina were able to force superstar winger Marcus Moneta into space and he broke the deadlock with three minutes to play.
The Blitzboks again failed to regain possession from the restart and Argentina scored a second try to dispatch their opponents.
The match against Kenya started well for South Africa as Soyizwapi scored twice in the first half before Kenya pulled one back before the break.
The 12-5 lead remained intact until the 13thTh minute when the Kenyans scored a try converted to level the score at 12-12.
Again, from the restart, the Blitzboks cleared the line and Kenya raced to try and win.
In the Cup competition, Argentina will face Ireland in the semi-finals on Sunday, while France face Australia.
Score summary:
South Africa 0 (0), Argentina 12 (0)
Argentina – Tried: Marcus Moneta, German Schulz. Conversion: Joaquin Pellandini.
South Africa 12 (12), Kenya 17 (5)
South Africa – Tried: Siviwe Soyizwapi (2). Conversion: Ricardo Duartee.
Kenya – Try: George Ooro Angeyo, Brian Tanga, John Okoth. Conversion: Anthony Mondi.