He will also take out the prestigious Triple Crown of Surfing ahead of fellow Australian Ethan Ewing and Hawaiian Ezekiel Lau.
“I’m comfortable with whatever … and if I don’t win then hopefully I can be a good back-up for Team Australia,” Freestone said.
Wilson started his heat well, threading a short barrel and catching another small wave for a 4.17 and a 2.10 to put himself up 6.27 to 2.00 over the Brazilian.
But Dora took the lead off the 2014 Pipe Master champion by dropping deep behind the curtain and finishing with a frontside hack for a 5.50.
Wilson then dropped into a hollow left but he failed to see daylight as the wave clamped down on him.
The Australian was ready to go again, but the ocean went flat as the clock ticked down, failing to offer him another decent chance as Dora held priority.
In the earlier heat, world No.1 Italo Ferriera beat Brazilian compatriot Peterson Crisanto to keep his world title hopes alive.
Kelly Slater, the 13-time world champion, progressed to the quarter-finals after being pushed to the final minute for a win over Hawaiian Seth Moniz.
Australian Soli Bailey was taking on Pipeline local and double world champion John John Florence for a place in the last eight, while world title contender Gabriel Medina up against fellow Brazilian Caio Ibelli for the place in the next round.