The Palace 'keeper was the hero again just five minutes later, denying Tomas Costa from scoring with his shot from the edge of the box.
Palace responded with chances of their own in the closing stages. Second-half substitute Akinwale had two quickfire chances, one being an acrobatic overhead kick, but neither managed to test Fontes in the Braga goal.
In the third and final minute of time added on, David Ozoh won the ball on the right-wing and played it across the box to captain Jack Wells-Morrison who placed it in the top corner with aplomb - securing all three points and sealing qualification for the Eagles late on.
Palace U21s will now progress to the next round of the Premier League International Cup, finishing as runners-up in their group with nine points from their four games against European opposition.
Crystal Palace: Whitworth, Imray, Grehan, Watson, Balmer, Adaramola, Ozoh, Wells-Morrison, Omilabu (Akinwale, 73), Ola-Adebomi, Mooney (Rodney, 66)
Subs not used: Addae, Izquierdo, Kporha, Cadogan, Raymond.
SC Braga: Fontes, Casimiro, Pereira (Vilela, 85), Soares, Goncalves, T Costa (Fale, 85), Cunha, Moreira (Fernandes, 62), Jean-Marie (Eiro, 62), Said (Couto, 85), Lacximicant
Subs not used: Pinto, Machado.