Vilanova, taking control of only his third competitive match since replacing Pep Guardiola, was sent to the stands in the 70th minute of the match for what the referee's report claimed was "angrily protesting a play during the match after being warned by the assistant referee".
However, Vilanova says he was only calling for a foul and Barcelona have decided to appeal against the ruling.
Barca won the match 2-1 after trailing at half-time, with Lionel Messi netting both of his side's goals in the 75th and 80th minutes.
“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.