Vilanova, who was making his away debut in the league after taking over from Pep Guardiola at the end of last season, was sent from the bench in the second half when he protested the referee's decision not to award a free kick for a challenge on Sergio Busquets.
The referee said in his match report he had punished Vilanova "for angrily protesting a passage of play, having been warned by the fourth official".
"The expulsion was excessive because I didn't say anything that was out of line," Vilanova told a post-match news conference on Sunday.
"I told the linesman that it was a clear foul and he told me not to protest," he added.
"It seems that this is enough to get you booted from a game. All the managers in La Liga are warned, they know what will happen if they say there's a foul."