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That put Javi Gracia's men up against it, and they eventually fell behind when the Brazilian attacker finished off Antonio Barragan's cross moments before the break.
He scored his second three minutes after the restart, volleying home from Sofiane Feghouli's clipped ball into the box.
Jonas completed his hat-trick within the space of nine minutes by curling into Andres Fernandez's top corner from just inside the box.
It is the first time that any Brazilian has scored a hat-trick in Europe's top five leagues.
The result takes Los Che into ninth place in the table.