The Blitzboks lost 21-15 to Fiji in the Cup semi-finals of the Hong Kong Sevens, before overcoming Samoa in the third place play-off.
South Africa had earlier booked their place in the semis with a tense 7-5 win over Australia in the quarter-finals, but their quest for a first Hong Kong title fell agonisingly short against the Fijians, who went on to take the title against the Kiwis in the final.
The Blitzboks looked out of it at half-time as the islanders ran in three tries to lead 21-0. The physical Fijians were dominating possession and field position, and managed to put the Blitzboks under immense pressure in their own half.
However, tries from Frankie Horne and Cecil Afrika brought South Africa back into the match, but Branco du Preez failed to convert either try, meaning the Blitzboks needed two further tries to book their place in the final.
Justin Geduld looked to have got South Africa's third try, but it was ruled out for a forward pass from Kyle Brown, before Seabelo Senatla crossed with just over a minute remaining.
From the kick-off, Brown put in a massive tackle to hand South Africa a lineout and one last chance, but the throw failed to go to hand and the Fijians kicked the ball dead to seal their spot in the final.
The Blitzboks fell behind early against Samoa in the third-place play-off, but recovered through tries from Rosco Speckman, Stephan Dippenaar and a brace from Justin Geduld to run out comfortable winners.
The result means the Blitzboks maintain their position at the top of the World Series standings, although their lead is cut to just 2 points ahead of next weekend's stop in Japan.
Fiji 14 England 12
South Africa 7 Australia 5
USA 15 Samoa 26
New Zealand 31 Argentina 21
Fiji 21 South Africa 15
New Zealand 15 Samoa 14
South Africa 26 Samoa 7
New Zealand 19 Fiji 33
World Series standings (after six rounds):
1. South Africa 110
2. Fiji 108
3. New Zealand 107
4. Australia 84
5. England 78
6. Argentina 64
7. USA 63
8. Scotland 55
9. Samoa 51
10. France 44
Photo: Aitor Alcade/Getty Images