Unai Emery's side went into the break 0-2 in, but they turned around the score in the second half through Moi Gómez and Dani Raba.
In the 71st minute, when the home side were on top, a quick counter-attack by the Portuguese side saw them score the definitive goal, which made it 2-3. Fabiano was sent off for a challenge on Villarreal winger Arnaut Danjuma.
Villarreal CF will return to official competition next weekend, when they will face Deportivo Alavés on Matchday 4.
Villarreal CF: Sergio Asenjo, Mario Gaspar, Pau Torres, Dela, Pedraza, Rubén Peña, Iborra, Coquelin, Raba, Paco Alcácer.
Goals: 0-1. Min. 7: Vitinha. 0-2. Min. 24: Galeno. 1-2. Min. 51: Moi Gómez. 2-2. Min. 55: Raba. 2-3. Min. 72: Iuri Medeiros.
Referee: Iván Muñoz Pérez.
Sent off: Fabiano (SC Braga).
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