Man of the match Napolioni Bolaca scored all of Fiji's points in the first half as the Fijians secured their second win against the Blitzboks in eight days.
Bolaca, who was named in the tournament 'Dream Team' alongside Waisea Nacuqu, opened the scoring in the second minute, after pouncing on a ball that ball skewed out the side of a breakdown.
South Africa struck back two minutes later after a strong run from Zain Davids set up JC Pretorius to score, with Fiji's woes compounded after Josua Vakurunabili was shown a yellow card for a dangerous tackle earlier in the move.
But the men in white held firm on defence and, after being restored to their full compliment of players, Napolioni Bolaca doubled his tally with a stunning solo effort just before the interval, slicing through the South African defence and beating three defenders en-route to the tryline, to give Fiji a seven point buffer at half-time.
Zain Davids crossed for the Blitz Boks midway through the second spell but his namesake Selvyn was unable to add the conversion as Fiji held on to prevail by two points.
The result lifts the Fijians up to fifth place in the overall series standings and closes the gap on series leaders New Zealand to 23 points.
Captain Meli Derenalagi said their first ever Sydney title was a team effort.
"Before we entered the field the message I told my team was just to come out there, enjoy it and just do the job," he said.
"That's what we come and deliver it so I want to thank the soldiers behind me for the great effort that they showed today."
"It was quite challenging (to fill as captain in for the injured Paula Dranisinukula) but I thank my teammates behind me - the experience like Jerry Tuwai, Sevu Mocenecagi, Waisea Nacuqu for helping me leading the team."
A week after failing to qualify for the knockout rounds in Hamilton, Fiji defeated Kenya (28-14), series leaders New Zealand (26-5) and Wales (55-0) in pool play before edging England (17-14) in the Cup semis to reach their first final of the season.
The Fijiana also produced their best performance of the season in the women's draw, beating England 17-5 in the playoff for fifth place to climb to seventh in the competition standings, with Luisa Tisolo selected in the Sydney 'Dream Team'.
Meanwhile the Samoa men fell further off the pace after finishing a lowly 15th in Sydney.
For the second straight weekened, the Manu 7s lost all three pool matches against France (24-17), Argentina (28-21) and South Africa (36-0) before defeating Kenya 19-12 to avoid the wooden spoon.
The Men's World Series resumes in Los Angeles at the end of the month while the women's series takes an extended break