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The hosts could not profit from a few early chances and were punished in the 28th minute with a well-struck free kick from Xavi.
Mallorca got themselves back in the game in the 55th minute when Pereira dispatched Alfaro's cross. Three minutes later, the referee awarded Mallorca a penalty when Sergio Busquets handled inside the area.
Victor Casadesus put his penalty straight down the middle to restore yet more hope.
However, Messi's second goal of the night put the game to bed with 20 minutes remaining.