كتب : وكالات
The outsiders were inspired by a virtuoso perfromance from Brazilian striker Rodrigo Lima, who scored a second-half hat-trick to down the Spanish team.
"Braga were superior. We played two great games and last year we had a great season in Portugal," said Braga coach Domingos Paciencia.
Elsewhere, Werder Bremen booked their group stage place with a 5-4 aggregate win over Sampdoria, thanks to a vital Claudio Pizarro strike in extra time.
Belgian champions Anderlecht failed to make it as they were downed by Partizan Belgrade of Serbia, who went through on penalties.