It was a shock defeat for the 40-year-old, who is currently second in the world title race, as the 32-ranked Brazilian thrived at Supertubos.
Slater’s surprise elimination opens up the world title race for rivals Joel Parkinson and Mick Fanning of Australia, and Hawaii’s John John Florence.
"I don’t know what to say, it’s just luck of the draw sometimes,” Slater said. “I’m just a little upset at myself for even bothering. I shouldn’t even have paddled out to be honest. I should have said it’s so bad we couldn’t surf.
"It’s frustrating to go down without being able to get out-surfed or get the chances to out-surf someone else. Joel (Parkinson), Mick (Fanning) and John John (Florence) are really good in these conditions."
The world title will be awarded to the surfer with the best eight out of 10 ASP WCT results by the end of the year, and Slater’s disappointing showing in Portugal may count against him.
But although he was frustrated by his performance, Slater remained philosophical about his prospects at the final two events of the season: the O’Neill Cold Water Classic in Santa Cruz and the Billabong Pipeline Masters in Hawaii.
"It’s not the end of the world,” Slater said. “Nobody died, I just lost a heat. It’s a bummer for me, but it’s just the way it is.
"There’s only one way to go at Santa Cruz for me. I’ve surfed there once and I got last in my first heat, it was in 1994 I think. We’ll see what happens."
ROUND 3 RESULTS:
Heat 3: Kolohe Andino (USA) 12.50 def. Taj Burrow (AUS) 5.33
Heat 4: Josh Kerr (AUS) 13.24 def. Alejo Muniz (BRA) 10.50
Heat 5: Adrian Buchan (AUS) 11.33 def. C.J. Hobgood (USA) 10.43
Heat 6: Joel Parkinson (AUS) 14.73 def. Dusty Payne (HAW) 6.17
Heat 7: Raoni Monteiro (BRA) 9.20 def. Kelly Slater (USA) 5.27
Heat 8: Julian Wilson (AUS) 16.00 def. Michel Bourez (PYF) 10.23
Heat 9: Owen Wright (AUS) 16.27 def. Kai Otton (AUS) 9.83
Heat 10: Adriano de Souza (BRA) 12.43 def. Kieren Perrow (AUS) 11.33
Heat 11: Jeremy Flores (FRA) 13.27 def. Bede Durbidge (AUS) 10.60
Heat 12: Mick Fanning (AUS) 16.77 def. Yadin Nicol (AUS) 9.84
ROUND 4 RESULTS:
Heat 1: Gabriel Medina (BRA) 18.50, Kolohe Andino (USA) 12.80, John John Florence (HAW) 5.77
Heat 2: Joel Parkinson (AUS) 12.30, Adrian Buchan (AUS) 7.53, Josh Kerr (AUS) 6.26
Heat 3: Julian Wilson (AUS) 14.46, Owen Wright (AUS) 13.07, Raoni Monteiro (BRA) 12.40
Heat 4: Adriano de Souza (BRA) 13.10, Jeremy Flores (FRA) 13.06, Mick Fanning (AUS) 12.93
ROUND 5 RESULTS:
Heat 1: Josh Kerr (AUS) 16.57 def. Kolohe Andino (USA) 11.84
Heat 2: John John Florence (HAW) 17.03 def. Adrian Buchan (AUS) 5.80
Heat 3: Owen Wright (AUS) 18.00 def. Mick Fanning (AUS) 16.54
REMAINING ROUND 5 MATCH-UP:
Heat 4: Jeremy Flores (FRA) vs. Raoni Monteiro (BRA)
QF 1: Gabriel Medina (BRA) vs. Josh Kerr (AUS)
QF 2: Joel Parkinson (AUS) vs. John John Florence (HAW)
QF 3: Julian Wilson (AUS) vs. Owen Wright (AUS)
QF 4: Adriano de Souza (BRA) vs. TBD