The Brazilian forward, 24, was handed a second yellow card in the 65th minute for a reckless challenge on Diego Llorente.
Barcelona were already trailing at that point following Sandro Ramirez's opener, and the game was ended when Jhony netted in the dying seconds past Marc Andre ter Stegen to double the advantage.
At first there were suspicions that Neymar had received a straight red card, which would rule him out of April 23's Clasico at the Santiago Bernabeu.
However, referee Gil Manzano's report revealed he had been given a second yellow, following one from an original booking for obstructing a free kick by tying his laces.
The reason Neymar remains in hot water is due to his ironic clapping towards the fourth official following the red card, which could rule him out of Barca's matches against Real Sociedad and Real Madrid.
"After being sent off and on his way to the dressing room tunnel he turned clapping towards the fourth official," the report explains, after detailing the reasons for his two bookings.
And while a second yellow offence would lead to a one-match suspension, clearing him for the Clasico, he could miss the showpiece if La Liga's disciplinary committee further sanctions him for his reaction.
Barcelona are three points adrift of Zinedine Zidane's men having played a game more than their eternal rivals.