In July, Fanning survived a terrifying shark encounter during the final of the J-Bay Open and the event was cancelled, leaving him to share second place with Julian Wilson.
He didn’t miss any competition, despite the close call, but could only manage 13th place in Tahiti at the following round.
However, the Australian was back to his best at Trestles last week and his dominant performance in the final was enough to overcome de Souza, and knock him off the top spot in the rankings.
Fanning is now on course to lift his fourth WSL world title, with just three events remaining, and if he can hold on it will probably be his most satisfying yet.
“It’s been a wild year for me,” said Fanning. “To walk away with this trophy is really special. Adrian surfed amazing and he always puts up a huge fight.
“When you’re surfing on the Championship Tour you surf against the best in the world. A fourth world title won’t be easy.”
There are still plenty of contenders for the crown with de Souza less than 2,000 points behind Fanning in second and his fellow Brazilian Filipe Toledo in third.
Australians Owen Wright and Wilson are also in the top five and less than one win away from the number one spot, while 11-time world champion Kelly Slater sits in sixth and defending champion Gabriel Medina's recent form has helped him climb the rankings to seventh.
Carissa Moore has taken control of the rankings in the race for the women’s world title after beating Bianca Buitendag in the final.
The surfer from Hawaii now has three wins under her belt this season, and has only been off the podium twice in seven events.
“This is such a sweet win for me and I’m so, so stoked,” she said. “It’s shaping up to be a really exciting end of the year."