Messi, 31, was fuming with Jesus Gil Manzano after the man in the middle sent Clement Lenglet off in the first half.
The Argentina star had already put his side in front when, with ten minutes to go until half-time, Lenglet tangled with Pere Pons.
After consulting VAR, Manzano showed the Barcelona centre-back a red card.
And Messi was not afraid to let his feelings known to the ref after the full-time whistle.
He vented his frustrations before walking off without shaking the official's hand.
Barcelona surprisingly dropped points for the first time this season in the game at the Nou Camp.
Former Middlesbrough striker Christhian Stuani levelled for Girona on the stroke of half-time before putting the visitors in front six minutes after the break.
But Gerard Pique rescued a point for Barcelona, keeping them above Real Madrid on goal difference at the top of the La Liga table.
The return leg between Girona and fellow Catalan club Barca could be played in Miami but La Liga officials say there is a "0.0 per cent" chance of the game being moved to the United States.
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