South Africa, so impressive over the two days of the competition, won a thrilling final 26-14 as late tries from man of the match Chris Dry and the prolific Seabelo Senatla took them clear of the Fijians.
It was the fifth Dubai title for South Africa, which finished second to Fiji in the last two World Series and took bronze at the Rio Olympics.
Boks captain Philip Snyman said confidence was now high heading into the side's home round in Cape Town next weekend.
"We just needed to stick to our game plan and that's exactly what the guys did. We never let Fiji into the game and then they were playing catch-up rugby, which I think worked to our advantage," he told the official tournament website.
"We can be positive going into our home tournament next weekend in Cape Town, but we need to start all over again and fix a few things that went wrong."
Tries from Cecil Afrika and Branco du Preez gave his side an early advantage before Fiji captain Osea Kolinisau hit back with a converted score.
When Jerry Tuwai crossed under the posts for the Olympic gold medalists it looked ominous for South Africa, but Dry edged South Africa ahead before Senatla went over for his 11th try of the tournament.
In the third-place playoff, Dan Norton scored four of England's six tries in a 33-10 win over Wales.
Australia finished fifth while the US raised the men's Challenge Trophy with a 28-14 win over Samoa, the highlight being Perry Baker's crowd-pleasing first-half chip-and-chase try.
England equals Test best record
In 15-a-side international action Saturday, England stretched its unbeaten run to 14 games with a 37-21 win over Australia at Twickenham.
It equals a national record set in 2003, with 13 of the wins coming under Australian coach Eddie Jones, appointed after England's early exit at last year's World Cup.
England trailed 10-0 early on but tries from Jonathan Joseph (two), Marland Yarde and Ben Youngs led a sterling recovery to defeat the Wallabies for the fourth time this year.