The Brazilian suffered an injury to his left foot at the Mestalla but still finished the match.
On Tuesday, the medical staff at the Catalan club agreed that he could start training; however, it would be away from the squad, per AS.
He didn't make the session on Wednesday, which is a blow for Gerardo Martino's team selection.
I don’t just want him to play, I want Barca to be champions. Winning the League would improve his morale and his confidence, and with that the Brazilian team would also benefit. In addition, him playing would mean that he would be able to come into our squad with more match fitness.
In theory, it's a nice approach to take and a sign of his confidence in the winger ahead of the World Cup. Though, if he isn't fully fit and aggravates his injury further, the repercussions could be massive.
But that's not any of Barcelona's concern; they just need to get the best available players onto the pitch in order to beat Atletico Madrid on the weekend.
They don't want to push Neymar unnecessarily either; they want him to be ready for next season and to complete a full pre-season programme.
If he is in some way ready to play even a small part, it would be a huge addition for the club.
Mentally, Barca is struggling, but the sight of their big summer signing coming onto the pitch could be the psychological difference.
Neymar has had an indifferent campaign; he has scored nine goals and provided eight assists in La Liga during 19 starts.
The adaptation to a new continent, country, language, club and style was always going to take time.
It's even harder to learn the Barcelona philosophy when the coach and those around him are unsure of the right way forward.
Under a more stringent manager, it would have been easier to pick up the system and know his role exactly. That's not a criticism of Martino but an observation of his methods at Barcelona.
In a one-off match like against Atletico, Neymar has the skills to influence the game and the result, even though he wouldn't be firing on all cylinders.
When the two sides met at the Camp Nou in the Champions League, the wide man was on target and netted the away goal that gave Barca the Super Copa against the same opposition.
The opener in El Clasico provides further evidence that he is a scorer for the big occasion. Furthermore, only two of his goals were scored away from home this season.
You get a sense that he is a young man who values his home life and family. "The only thing that is certain is that I will end my career at Santos," Neymar told reporters recently, via Football Espana.
"It is something to think about whether I would be willing to play for another team in Brazil before that."
This talk of going back to his homeland won't appease supporters given the money spent on the player and the subsequent trouble caused.
The forward isn't looking for an exit; rather, he simply is trying to demonstrate his values and how fond he is of the club that gave him his footballing opportunity.
"It wasn't just about the money, that's not why I left. I wanted to live a dream, play other competitions, play the Champions League, grow, evolve, learn another language, that's what motivated me to come to the European continent."
Neymar will improve next season with a more guided structure, but for now, his unpredictability on the pitch is exactly what they need to unlock a rigid Atletico defence.