The 35-year-old Australian said the win over John John Florence of Hawaii completed an emotional circle 12 months after the incident that left surfing in shock and led to the abandonment of last year's final.
"Just coming back was a real rollercoaster of emotions but I'm stoked I got to come back and right the wrong," Fanning said in an emotional address after shooting up to fifth in the World Surf League rankings even though he is only competing in select events this year.
"That was my whole plan. To right the wrong that happened last year and now we can move on.
"The first thing to overcome was just getting out there and not being so petrified. It was really special to win."
Last year Fanning was attacked by a shark with live television pictures showing a 12- to 15-foot great white circling the three-time world champion and then appearing to knock him off his board.
As horrified spectators looked on, Fanning punched and kicked at the shark, before swimming toward a jet-ski which took him back to shore unscathed.
Within five days he was back in the water in his native Australia and despite the near-death escape, continued competing on the world circuit, finishing second at the end of the year.
Fanning shared the J-Bay Open title with Julian Wilson last year following the abandonment of the final and beat him earlier on Saturday in the semi-final.
In the final, Fanning scored 17.70 to Florence's 17.13 to win a 22nd championship tour victory and a $100,000 first prize.
Fellow surfers carried him on their shoulders after Fanning emerged victorious from the cold Indian Ocean water off the South African coast.
Florence, 23, gained 8,000 points for finishing runner-up and is now second in the WSF rankings, just 2,350 points behind leader Matt Wilkinson of Australia with five events left on this year's calendar.
