The pair survived on a day when fellow big names were bounced out of the ASP Prime event at Huntington Beach.
Pupo notched the opening round's highest heat total with an 18.07, largely thanks to a near-perfect 9.07 on a single wave.
Reigning 11-times world champion Kelly Slater also safely progressed but there were upsets elsewhere.
Australians Owen Wright and current world number one Mick Fanning were both dumped out, with Mitch Crews and Evan Geiselman winning their respective heats.
“I knew the waves were kind of slow and there was a long wait in between sets so I was getting everything I could,” Pupo said. “I was looking for the airs because, coming from Brazil, you learn how to get good scores in these types of waves.”
“There are some crazy heats in the first round and I saw Mick [Fanning] and Owen [Wright] go down, so I was kind of nervous. It’s such a difficult wave to surf and in these tough conditions, so I’m happy to make it through.”
Kerr topped Pupo's single-wave score with a 9.50 for an outside aerial and polished inside turn to safely negotiate his opening round heat.
“I really haven’t surfed since Fiji because of my injury and I’m still not feeling that great,” Kerr said. “I can do whatever I want, but I’m still not feeling 100 per cent. It has almost given me motivation and it was good to get a good start out there.”
Round of 96 results:
Heat 1: Evan Geiselman (USA) 14.86, Tanner Gudauskas (USA) 14.20, Nathan Hedge (AUS) 12.77, Mick Fanning (AUS) 6.66
Heat 2: Kai Otton (AUS) 11.93, Alain Riou (PYF) 7.23, Adrien Toyon (FRA) 6.93, Taylor Knox (USA) 3.37
Heat 3: Jay Thompson (AUS) 14.70, Tim Reyes (USA) 14.20, Adrian Buchan (AUS) 13.27, Nathan Yeomans (USA) 8.72
Heat 4: Mitch Crews (AUS) 16.70, Tomas Hermes (BRA) 12.77, Owen Wright (AUS) 12.64, Kekoa Bacalso (HAW) 11.13
Heat 5: Jordy Smith (ZAF) 16.67, Nathaniel Curran (USA) 12.10, Romain Cloitre (FRA) 8.64, Joel Centeio (HAW) 7.24
Heat 6: Miguel Pupo (BRA) 18.07, Fredrick Patacchia (HAW) 13.56, Maxime Huscenot (FRA) 10.36, Charles Martin (GLP) 8.53
Heat 7: Kiron Jabour (HAW) 13.60, Bede Durbidge (AUS) 12.60, Shaun Joubert (ZAF) 9.93, Glenn Hall (IRL) 8.96
Heat 8: Dane Reynolds (USA) 13.53, Filipe Toledo (BRA) 10.22, Jack Freestone (AUS) 9.73, Taj Burrow (AUS) 8.60
Heat 9: Daniel Ross (AUS) 11.43, Sebastien Zietz (HAW) 10.87, C.J. Hobgood (USA) 10.80, Cory Lopez (USA) 7.76
Heat 10: Jesse Mendes (BRA) 13.60, Michel Bourez (PYF) 11.54, Joan Duru (FRA) 11.50, Garrett Parkes (AUS) 6.73
Heat 11: Stu Kennedy (AUS) 12.90, Yadin Nicol (AUS) 11.14, Matt Wilkinson (AUS) 8.50, Hodei Collazo (EUK) 6.71
Heat 12: Kelly Slater (USA) 15.20, Jay Quinn (NZL) 12.90, Torrey Meister (HAW) 12.37, Chris Ward (USA) 11.57
Heat 13: Dion Atkinson (AUS) 16.50, Adriano de Souza (BRA) 16.24, Tom Whitaker (AUS) 14.43, Jean Da Silva (BRA) 12.47
Heat 14: Adam Melling (AUS) 15.43, Thiago Camarao (BRA) 9.70, Gony Zubizarreta (ESP) 9.67, Jadson Andre (BRA) 9.19
Heat 15: Heitor Alves (BRA) 14.94, Alex Ribeiro (BRA) 10.80, Hank Gaskell (HAW) 10.44, Blake Thornton (AUS) 4.88
Heat 16: Granger Larsen (HAW) 16.80, Gabriel Medina (BRA) 14.56, Conner Coffin (AUS) 13.76, Aritz Aranburu (EUK) 8.27
Heat 17: Josh Kerr (AUS) 18.00, Gabe Kling (USA) 13.27, Andrew Doheny (USA) 11.83, Mason Ho (HAW) 7.00
Heat 18: Willian Cardoso (BRA) 14.00, Caio Ibelli (BRA) 12.00, Damien Hobgood (USA) 8.60, Marc Lacomare (FRA) 7.00