Andre, 22, narrowly edged out the Australian two-times ASP world champion with a furious combination of backhand blasts that gave him the seven-point ride he needed.
The result puts a significant dampener on WCT number three Fanning’s world title campaign.
"I knew that was going to be a hard heat. Mick was looking for the World Title and I’m trying to keep myself on the World Tour," Andre said.
"It was an important heat for both Mick (Fanning) and myself. Mick started with a 9 and I was wondering what’s going on. All of my heats, people are starting with 10s and 9.5s. I tried to stay focused and knew I could get the score if I had the opportunity."
But Andre couldn’t continue the momentum and was eliminated by veteran Australian Taj Burrow in round three, finishing in equal 13th place.
The day’s shake-ups continued when 2010 tournament winner Matt Wilkinson sent WCT number four John Florence on his way, at the same time ending the 19-year-old Hawaiian’s chances this year.
Wilkinson put in a seamless backhand performance and a flurry of turns to take one of the day’s highest scores at 9.20.
"I know I can get big scores out here and I kind of know which waves are good," Wilkinson said.
"It’s a really tricky wave and there are so many elements that can make a good wave bad. It was a relief when I got that nine. I started off on a wave that I thought was perfect and there was so much wonky stuff going on.
"I just decided to wait for a bomb and when that one was coming I was super nervous. I knew if I just surfed it I’d get an eight. It was a perfect wave and I got a good score so I’m stoked."
Current world number one Joel Parkinson and 11-times ASP world champion Kelly Slater came out on top in their heats to further intensify the race for the 2012 crown.
Australia’s Parkinson looked confident, showing off his signature forehand approach to trounce dangerous local wildcard Nat Young.
Slater, meanwhile, had struggled to find a rhythm on Friday, leading him to be stunned by 21-year-old Young and relegated to the second round.
But the American slowly regained form with a narrow victory over wildcard Jason Collins in round two before convincingly reigning supreme in his round-three stand-off with Hawaiian Dusty Payne.
“There’s a very good chance that I’m out of the race if I don’t win a couple of heats here,” Slater said after his round two win.
“With that being said, it’s easier for me to make up points if I start getting results. If I make quarters or better, I’ll add some good points.”
Round two results:
Heat 1: Kelly Slater (USA) 11.20, Jason Collins (USA) 9.40
Heat 2: Jadson Andre (BRA) 14.10, Mick Fanning (AUS) 14.06
Heat 3: Matt Wilkinson (AUS) 14.50, John John Florence (HAW) 8.66
Heat 4: Adriano de Souza (BRA) 13.43, Adam Melling (AUS) 11.50
Heat 5: Raoni Monteiro (BRA) 14.44, Julian Wilson (AUS) 13.67
Heat 6: Owen Wright (AUS) 10.63, Tiago Pires (PRT) 8.27
Heat 7: Damien Hobgood (USA) 15.50, Josh Kerr (AUS) 12.94
Heat 8: Jeremy Flores (FRA) 13.47, Kolohe Andino (USA) 12.53
Heat 9: Adrian Buchan (AUS) 18.33, Kieren Perrow (AUS) 12.60
Heat 10: C.J. Hobgood (USA) 12.17, Heitor Alves (BRA) 10.53
Heat 11: Alejo Muniz (BRA) 15.10, Miguel Pupo (BRA) 15.06
Heat 12: Bede Durbidge (AUS) 13.40, Brett Simpson (USA) 9.07
Round three results:
Heat 1: Taj Burrow (AUS) 14.83, Jadson Andre (BRA) 12.17
Heat 2: Travis Logie (ZAF) 14.67, Adrian Buchan (AUS) 11.13
Heat 3: Gabriel Medina (BRA) 16.53, Taylor Knox (USA) 14.77
Heat 4: Raoni Monteiro (BRA) 11.10, Jordy Smith (ZAF) 10.23
Heat 5: Alejo Muniz (BRA) 13.33, Bede Durbidge (AUS) 11.30
Heat 6: Joel Parkinson (AUS) 15.63, Nat Young (USA) 12.43
Heat 7: Kelly Slater (USA) 15.84, Dusty Payne (HAW) 14.77
Heat 8: Michel Bourez (PYF) 12.40, Kai Otton (AUS) 5.27