The final was played in a downpour at Bankwest Stadium and this resulted in a tight affair. Fiji scored twice in the first half and although the South Africans rallied in the second half, that proved decisive.
After Fiji scored an early converted try, JC Pretorius responded with his seventh try of the weekend to cut the lead to two.
Fiji extended the lead with a well-worked move from a line-out to lead 12-5 at the break.
Zain Davids scored out wide late in the second half, but that still left the Blitzboks two points short and hard as they tried, the final scoring act did not come and Fiji could celebrate.
The final appearance marked South Africa’s third in four tournaments thanks to a 19-12 win over USA in the semi-final, after closing out Samoa 36-0 in their final pool match.
The win over Samoa confirmed their passage to the top four, as all the pool winners qualified automatically for the semi-finals.
Fiji, who eliminated New Zealand by topping their pool, outplayed England to advance to the final.
The Blitzboks showed good determination against the USA and their discipline on defence proved decisive.
They scored in the first minute when JC Pretorius caught the USA defence napping straight from the kick-off for a 5-0 lead.
That was wiped out by the USA in the blink of an eye though. First the Americans scored a well-worked try through Martin Iosefo, and from the resulting restart, Ben Pinkelman scored after a mix-up amongst the South Africans.
Their 12-5 lead was overturned by Davids, who chipped-and-chased successfully against the flat American line, exploiting the fact that they had no sweeper in place.
The second half was a hard-fought affair. Rain came down and that added to the drama, but once Stedman Gans stepped hard on his right foot to score under the posts for a 19-12 lead, it was time for the defence to close out the game, which they did.
Against Samoa, JC Pretorius and Angelo Davids both earned braces. Davids, who scored two hat-tricks on Saturday, was denied his third when his foot touched the line, while Selvyn Davids and Muller du Plessis also enjoyed the momentum coming from the forwards to score good tries.
Impi Visser picked up a knock against Samoa and was ruled out for the final two matches. Sako Makata replaced him.
South Africa 10 (5), Fiji 12 (12)
South Africa - Tries: JC Pretorius, Zain Davids
Fiji - Tries: Napolioni Bolaca (2). Conversion: Bolaca
South Africa 19 (12), USA 12 (12)
South Africa - Tries: JC Pretorius, Selvyn Davids, Stedman Gans. Conversions: Selvyn Davids (2)
USA - Tries: Martin Iosefo, Ben Pinkelman. Conversion: Cody Melphy.
South Africa 36 (19), Samoa 0 (0)
South Africa - Tries: JC Pretorius (2), Selvyn Davids, Angelo Davids (2), Muller du Plessis. Conversions: Selvyn Davids (2), Branco Du Preez.